Starting phenix.real_space_refine on Sun Jul 21 05:17:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jrq_36602/07_2024/8jrq_36602_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jrq_36602/07_2024/8jrq_36602.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jrq_36602/07_2024/8jrq_36602.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jrq_36602/07_2024/8jrq_36602.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jrq_36602/07_2024/8jrq_36602_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jrq_36602/07_2024/8jrq_36602_neut.cif" } resolution = 4.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 92 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 76 5.16 5 C 8444 2.51 5 N 2248 2.21 5 O 2498 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 131": "OE1" <-> "OE2" Residue "A GLU 135": "OE1" <-> "OE2" Residue "A GLU 138": "OE1" <-> "OE2" Residue "A ARG 141": "NH1" <-> "NH2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 411": "OE1" <-> "OE2" Residue "A GLU 416": "OE1" <-> "OE2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A GLU 452": "OE1" <-> "OE2" Residue "A GLU 546": "OE1" <-> "OE2" Residue "A GLU 727": "OE1" <-> "OE2" Residue "A GLU 860": "OE1" <-> "OE2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C GLU 135": "OE1" <-> "OE2" Residue "C GLU 138": "OE1" <-> "OE2" Residue "C ARG 141": "NH1" <-> "NH2" Residue "C GLU 250": "OE1" <-> "OE2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 411": "OE1" <-> "OE2" Residue "C GLU 416": "OE1" <-> "OE2" Residue "C GLU 429": "OE1" <-> "OE2" Residue "C GLU 452": "OE1" <-> "OE2" Residue "C GLU 546": "OE1" <-> "OE2" Residue "C GLU 727": "OE1" <-> "OE2" Residue "C GLU 860": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 13270 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1191 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "A" Number of atoms: 5442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5442 Classifications: {'peptide': 676} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 27, 'TRANS': 648} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1191 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "C" Number of atoms: 5442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5442 Classifications: {'peptide': 676} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 27, 'TRANS': 648} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 241 SG CYS B 37 68.309 32.585 95.791 1.00112.82 S ATOM 522 SG CYS B 70 65.473 35.707 93.423 1.00109.09 S ATOM 864 SG CYS B 110 65.476 31.891 77.991 1.00 99.70 S ATOM 886 SG CYS B 113 63.164 30.431 80.490 1.00107.26 S ATOM 1148 SG CYS B 143 61.168 31.418 77.705 1.00129.08 S ATOM 1168 SG CYS B 146 62.382 34.471 79.323 1.00135.09 S ATOM 6874 SG CYS D 37 75.205 72.373 95.791 1.00112.82 S ATOM 7155 SG CYS D 70 78.041 69.251 93.423 1.00109.09 S ATOM 7497 SG CYS D 110 78.038 73.067 77.991 1.00 99.70 S ATOM 7519 SG CYS D 113 80.350 74.527 80.490 1.00107.26 S ATOM 7781 SG CYS D 143 82.346 73.540 77.705 1.00129.08 S ATOM 7801 SG CYS D 146 81.132 70.487 79.323 1.00135.09 S Time building chain proxies: 7.82, per 1000 atoms: 0.59 Number of scatterers: 13270 At special positions: 0 Unit cell: (144.585, 106.029, 111.384, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 76 16.00 O 2498 8.00 N 2248 7.00 C 8444 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.16 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 201 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 37 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 70 " pdb=" ZN B 202 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 113 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 110 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 146 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 143 " pdb=" ZN D 201 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 37 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 70 " pdb=" ZN D 202 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 113 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 110 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 146 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 143 " Number of angles added : 12 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3136 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 12 sheets defined 57.5% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'B' and resid 18 through 23 Processing helix chain 'B' and resid 45 through 55 removed outlier: 4.074A pdb=" N ALA B 53 " --> pdb=" O VAL B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 85 removed outlier: 3.528A pdb=" N PHE B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 99 removed outlier: 4.376A pdb=" N GLU B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN B 97 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 106 Processing helix chain 'B' and resid 120 through 128 removed outlier: 3.771A pdb=" N HIS B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 148 removed outlier: 4.185A pdb=" N ARG B 148 " --> pdb=" O SER B 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 141 Processing helix chain 'A' and resid 148 through 156 removed outlier: 4.579A pdb=" N VAL A 156 " --> pdb=" O VAL A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 166 removed outlier: 3.857A pdb=" N VAL A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A 166 " --> pdb=" O ALA A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 243 removed outlier: 3.667A pdb=" N ILE A 239 " --> pdb=" O ASP A 235 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 240 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARG A 241 " --> pdb=" O ASP A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 273 removed outlier: 3.723A pdb=" N ASN A 258 " --> pdb=" O THR A 254 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU A 260 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR A 262 " --> pdb=" O ASN A 258 " (cutoff:3.500A) Proline residue: A 265 - end of helix removed outlier: 4.243A pdb=" N ASP A 270 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.918A pdb=" N ARG A 279 " --> pdb=" O ASN A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 292 removed outlier: 3.958A pdb=" N ILE A 288 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 289 " --> pdb=" O ASN A 285 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 Proline residue: A 299 - end of helix removed outlier: 3.543A pdb=" N LEU A 302 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU A 303 " --> pdb=" O GLU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 315 removed outlier: 4.381A pdb=" N LEU A 308 " --> pdb=" O MET A 304 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 328 Processing helix chain 'A' and resid 329 through 331 No H-bonds generated for 'chain 'A' and resid 329 through 331' Processing helix chain 'A' and resid 332 through 354 removed outlier: 3.733A pdb=" N PHE A 343 " --> pdb=" O MET A 339 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE A 352 " --> pdb=" O THR A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 386 removed outlier: 3.788A pdb=" N VAL A 369 " --> pdb=" O ASP A 365 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL A 383 " --> pdb=" O TYR A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 413 removed outlier: 3.528A pdb=" N GLN A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 433 Processing helix chain 'A' and resid 435 through 439 Processing helix chain 'A' and resid 445 through 449 Processing helix chain 'A' and resid 459 through 469 removed outlier: 3.884A pdb=" N ASP A 463 " --> pdb=" O GLU A 459 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR A 465 " --> pdb=" O ASP A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 484 Proline residue: A 481 - end of helix Processing helix chain 'A' and resid 488 through 514 removed outlier: 3.907A pdb=" N THR A 508 " --> pdb=" O GLU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 546 removed outlier: 4.041A pdb=" N VAL A 538 " --> pdb=" O ASP A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 553 removed outlier: 4.010A pdb=" N LEU A 551 " --> pdb=" O PRO A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 583 removed outlier: 3.996A pdb=" N PHE A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLN A 576 " --> pdb=" O LYS A 572 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 625 removed outlier: 3.655A pdb=" N LEU A 614 " --> pdb=" O GLY A 610 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE A 615 " --> pdb=" O GLN A 611 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY A 616 " --> pdb=" O PHE A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 643 removed outlier: 3.970A pdb=" N TYR A 638 " --> pdb=" O PRO A 634 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET A 642 " --> pdb=" O TYR A 638 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY A 643 " --> pdb=" O ARG A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 655 removed outlier: 3.675A pdb=" N SER A 654 " --> pdb=" O ASP A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 667 removed outlier: 3.718A pdb=" N SER A 661 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU A 665 " --> pdb=" O SER A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 723 removed outlier: 4.634A pdb=" N ASP A 719 " --> pdb=" O ASN A 715 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE A 721 " --> pdb=" O TYR A 717 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU A 722 " --> pdb=" O SER A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 742 removed outlier: 4.251A pdb=" N VAL A 740 " --> pdb=" O GLY A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 750 Processing helix chain 'A' and resid 751 through 760 removed outlier: 3.850A pdb=" N GLU A 756 " --> pdb=" O PRO A 752 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU A 757 " --> pdb=" O GLU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 773 removed outlier: 3.639A pdb=" N GLU A 772 " --> pdb=" O GLN A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 797 removed outlier: 4.352A pdb=" N ARG A 788 " --> pdb=" O SER A 784 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N PHE A 790 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TRP A 791 " --> pdb=" O ILE A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 810 removed outlier: 4.251A pdb=" N PHE A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR A 809 " --> pdb=" O PHE A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 867 Processing helix chain 'D' and resid 18 through 23 Processing helix chain 'D' and resid 45 through 55 removed outlier: 4.074A pdb=" N ALA D 53 " --> pdb=" O VAL D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 85 removed outlier: 3.528A pdb=" N PHE D 76 " --> pdb=" O LYS D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 99 removed outlier: 4.376A pdb=" N GLU D 96 " --> pdb=" O GLY D 92 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 106 Processing helix chain 'D' and resid 120 through 128 removed outlier: 3.771A pdb=" N HIS D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 148 removed outlier: 4.185A pdb=" N ARG D 148 " --> pdb=" O SER D 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 141 Processing helix chain 'C' and resid 148 through 156 removed outlier: 4.579A pdb=" N VAL C 156 " --> pdb=" O VAL C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 166 removed outlier: 3.857A pdb=" N VAL C 164 " --> pdb=" O ALA C 160 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER C 166 " --> pdb=" O ALA C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 243 removed outlier: 3.667A pdb=" N ILE C 239 " --> pdb=" O ASP C 235 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG C 240 " --> pdb=" O ILE C 236 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARG C 241 " --> pdb=" O ASP C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 273 removed outlier: 3.723A pdb=" N ASN C 258 " --> pdb=" O THR C 254 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU C 260 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR C 262 " --> pdb=" O ASN C 258 " (cutoff:3.500A) Proline residue: C 265 - end of helix removed outlier: 4.243A pdb=" N ASP C 270 " --> pdb=" O ASN C 266 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU C 271 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 280 removed outlier: 3.918A pdb=" N ARG C 279 " --> pdb=" O ASN C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 292 removed outlier: 3.958A pdb=" N ILE C 288 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE C 289 " --> pdb=" O ASN C 285 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 303 Proline residue: C 299 - end of helix removed outlier: 3.543A pdb=" N LEU C 302 " --> pdb=" O PRO C 299 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU C 303 " --> pdb=" O GLU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 315 removed outlier: 4.381A pdb=" N LEU C 308 " --> pdb=" O MET C 304 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE C 309 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 328 Processing helix chain 'C' and resid 329 through 331 No H-bonds generated for 'chain 'C' and resid 329 through 331' Processing helix chain 'C' and resid 332 through 354 removed outlier: 3.733A pdb=" N PHE C 343 " --> pdb=" O MET C 339 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL C 351 " --> pdb=" O ILE C 347 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE C 352 " --> pdb=" O THR C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 386 removed outlier: 3.788A pdb=" N VAL C 369 " --> pdb=" O ASP C 365 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET C 377 " --> pdb=" O LYS C 373 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL C 383 " --> pdb=" O TYR C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 413 removed outlier: 3.528A pdb=" N GLN C 410 " --> pdb=" O GLU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 433 Processing helix chain 'C' and resid 435 through 439 Processing helix chain 'C' and resid 445 through 449 Processing helix chain 'C' and resid 459 through 469 removed outlier: 3.884A pdb=" N ASP C 463 " --> pdb=" O GLU C 459 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR C 465 " --> pdb=" O ASP C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 484 Proline residue: C 481 - end of helix Processing helix chain 'C' and resid 488 through 514 removed outlier: 3.907A pdb=" N THR C 508 " --> pdb=" O GLU C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 546 removed outlier: 4.041A pdb=" N VAL C 538 " --> pdb=" O ASP C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 553 removed outlier: 4.010A pdb=" N LEU C 551 " --> pdb=" O PRO C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 583 removed outlier: 3.996A pdb=" N PHE C 575 " --> pdb=" O SER C 571 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLN C 576 " --> pdb=" O LYS C 572 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU C 580 " --> pdb=" O GLN C 576 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 625 removed outlier: 3.655A pdb=" N LEU C 614 " --> pdb=" O GLY C 610 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE C 615 " --> pdb=" O GLN C 611 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY C 616 " --> pdb=" O PHE C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 643 removed outlier: 3.970A pdb=" N TYR C 638 " --> pdb=" O PRO C 634 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET C 642 " --> pdb=" O TYR C 638 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY C 643 " --> pdb=" O ARG C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 655 removed outlier: 3.675A pdb=" N SER C 654 " --> pdb=" O ASP C 650 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 667 removed outlier: 3.718A pdb=" N SER C 661 " --> pdb=" O VAL C 657 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU C 665 " --> pdb=" O SER C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 723 removed outlier: 4.634A pdb=" N ASP C 719 " --> pdb=" O ASN C 715 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE C 721 " --> pdb=" O TYR C 717 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU C 722 " --> pdb=" O SER C 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 726 through 742 removed outlier: 4.251A pdb=" N VAL C 740 " --> pdb=" O GLY C 736 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 750 Processing helix chain 'C' and resid 751 through 760 removed outlier: 3.850A pdb=" N GLU C 756 " --> pdb=" O PRO C 752 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU C 757 " --> pdb=" O GLU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 767 through 773 removed outlier: 3.639A pdb=" N GLU C 772 " --> pdb=" O GLN C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 784 through 797 removed outlier: 4.352A pdb=" N ARG C 788 " --> pdb=" O SER C 784 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N PHE C 790 " --> pdb=" O LEU C 786 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TRP C 791 " --> pdb=" O ILE C 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 810 removed outlier: 4.251A pdb=" N PHE C 808 " --> pdb=" O LEU C 804 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR C 809 " --> pdb=" O PHE C 805 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 867 Processing sheet with id=AA1, first strand: chain 'B' and resid 60 through 61 Processing sheet with id=AA2, first strand: chain 'B' and resid 86 through 88 removed outlier: 3.679A pdb=" N TYR B 88 " --> pdb=" O ASN B 134 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ARG B 109 " --> pdb=" O GLY B 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 523 through 527 removed outlier: 5.810A pdb=" N LEU A 523 " --> pdb=" O TYR A 556 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLU A 558 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N LEU A 525 " --> pdb=" O GLU A 558 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 590 through 593 removed outlier: 3.563A pdb=" N LEU A 598 " --> pdb=" O ASP A 593 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 681 through 685 Processing sheet with id=AA6, first strand: chain 'A' and resid 828 through 829 removed outlier: 6.724A pdb=" N ALA A 828 " --> pdb=" O LEU A 849 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 60 through 61 Processing sheet with id=AA8, first strand: chain 'D' and resid 86 through 88 removed outlier: 3.679A pdb=" N TYR D 88 " --> pdb=" O ASN D 134 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ARG D 109 " --> pdb=" O GLY D 141 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 523 through 527 removed outlier: 5.810A pdb=" N LEU C 523 " --> pdb=" O TYR C 556 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLU C 558 " --> pdb=" O LEU C 523 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N LEU C 525 " --> pdb=" O GLU C 558 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 590 through 593 removed outlier: 3.563A pdb=" N LEU C 598 " --> pdb=" O ASP C 593 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 681 through 685 Processing sheet with id=AB3, first strand: chain 'C' and resid 828 through 829 removed outlier: 6.724A pdb=" N ALA C 828 " --> pdb=" O LEU C 849 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 502 hydrogen bonds defined for protein. 1392 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.52 Time building geometry restraints manager: 5.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4358 1.34 - 1.46: 2828 1.46 - 1.58: 6220 1.58 - 1.70: 0 1.70 - 1.82: 116 Bond restraints: 13522 Sorted by residual: bond pdb=" N ARG A 763 " pdb=" CA ARG A 763 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.16e-02 7.43e+03 8.95e+00 bond pdb=" N ARG C 763 " pdb=" CA ARG C 763 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.16e-02 7.43e+03 8.95e+00 bond pdb=" N VAL C 362 " pdb=" CA VAL C 362 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.22e-02 6.72e+03 8.80e+00 bond pdb=" N VAL A 362 " pdb=" CA VAL A 362 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.22e-02 6.72e+03 8.80e+00 bond pdb=" N LEU A 361 " pdb=" CA LEU A 361 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.25e-02 6.40e+03 8.39e+00 ... (remaining 13517 not shown) Histogram of bond angle deviations from ideal: 99.80 - 106.69: 328 106.69 - 113.59: 7306 113.59 - 120.48: 5790 120.48 - 127.38: 4748 127.38 - 134.28: 88 Bond angle restraints: 18260 Sorted by residual: angle pdb=" N VAL A 726 " pdb=" CA VAL A 726 " pdb=" C VAL A 726 " ideal model delta sigma weight residual 111.88 106.75 5.13 1.06e+00 8.90e-01 2.34e+01 angle pdb=" N VAL C 726 " pdb=" CA VAL C 726 " pdb=" C VAL C 726 " ideal model delta sigma weight residual 111.88 106.75 5.13 1.06e+00 8.90e-01 2.34e+01 angle pdb=" N ARG A 782 " pdb=" CA ARG A 782 " pdb=" C ARG A 782 " ideal model delta sigma weight residual 111.28 115.60 -4.32 1.09e+00 8.42e-01 1.57e+01 angle pdb=" N ARG C 782 " pdb=" CA ARG C 782 " pdb=" C ARG C 782 " ideal model delta sigma weight residual 111.28 115.60 -4.32 1.09e+00 8.42e-01 1.57e+01 angle pdb=" C THR A 798 " pdb=" N ASP A 799 " pdb=" CA ASP A 799 " ideal model delta sigma weight residual 120.38 125.59 -5.21 1.37e+00 5.33e-01 1.44e+01 ... (remaining 18255 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 7098 17.48 - 34.96: 956 34.96 - 52.44: 168 52.44 - 69.92: 36 69.92 - 87.40: 16 Dihedral angle restraints: 8274 sinusoidal: 3436 harmonic: 4838 Sorted by residual: dihedral pdb=" CA SER A 784 " pdb=" C SER A 784 " pdb=" N VAL A 785 " pdb=" CA VAL A 785 " ideal model delta harmonic sigma weight residual -180.00 -152.25 -27.75 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA SER C 784 " pdb=" C SER C 784 " pdb=" N VAL C 785 " pdb=" CA VAL C 785 " ideal model delta harmonic sigma weight residual -180.00 -152.25 -27.75 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA ALA A 238 " pdb=" C ALA A 238 " pdb=" N ILE A 239 " pdb=" CA ILE A 239 " ideal model delta harmonic sigma weight residual -180.00 -153.78 -26.22 0 5.00e+00 4.00e-02 2.75e+01 ... (remaining 8271 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1696 0.077 - 0.154: 290 0.154 - 0.230: 24 0.230 - 0.307: 2 0.307 - 0.384: 2 Chirality restraints: 2014 Sorted by residual: chirality pdb=" CB ILE C 401 " pdb=" CA ILE C 401 " pdb=" CG1 ILE C 401 " pdb=" CG2 ILE C 401 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CB ILE A 401 " pdb=" CA ILE A 401 " pdb=" CG1 ILE A 401 " pdb=" CG2 ILE A 401 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CB ILE C 793 " pdb=" CA ILE C 793 " pdb=" CG1 ILE C 793 " pdb=" CG2 ILE C 793 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 2011 not shown) Planarity restraints: 2372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 444 " 0.048 5.00e-02 4.00e+02 7.34e-02 8.63e+00 pdb=" N PRO C 445 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO C 445 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 445 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 444 " -0.048 5.00e-02 4.00e+02 7.34e-02 8.63e+00 pdb=" N PRO A 445 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 445 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 445 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 751 " 0.043 5.00e-02 4.00e+02 6.46e-02 6.68e+00 pdb=" N PRO C 752 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO C 752 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 752 " 0.035 5.00e-02 4.00e+02 ... (remaining 2369 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2108 2.75 - 3.29: 13268 3.29 - 3.82: 22940 3.82 - 4.36: 27721 4.36 - 4.90: 43955 Nonbonded interactions: 109992 Sorted by model distance: nonbonded pdb=" N CYS B 70 " pdb="ZN ZN B 201 " model vdw 2.210 2.310 nonbonded pdb=" N CYS D 70 " pdb="ZN ZN D 201 " model vdw 2.210 2.310 nonbonded pdb=" O SER C 476 " pdb=" OG1 THR C 479 " model vdw 2.259 2.440 nonbonded pdb=" O SER A 476 " pdb=" OG1 THR A 479 " model vdw 2.259 2.440 nonbonded pdb=" OD1 ASN C 485 " pdb=" OG1 THR C 488 " model vdw 2.260 2.440 ... (remaining 109987 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 39.610 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 13522 Z= 0.466 Angle : 1.091 11.295 18260 Z= 0.625 Chirality : 0.058 0.384 2014 Planarity : 0.007 0.073 2372 Dihedral : 16.229 87.399 5138 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 0.69 % Allowed : 12.26 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.43 (0.16), residues: 1610 helix: -3.55 (0.12), residues: 748 sheet: -3.93 (0.40), residues: 64 loop : -2.12 (0.19), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP D 139 HIS 0.005 0.002 HIS C 632 PHE 0.025 0.003 PHE C 633 TYR 0.029 0.003 TYR A 134 ARG 0.008 0.001 ARG C 836 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 1514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 557 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 CYS cc_start: 0.6979 (m) cc_final: 0.6684 (m) REVERT: B 79 LYS cc_start: 0.8271 (tppt) cc_final: 0.7222 (tppt) REVERT: B 108 ILE cc_start: 0.8087 (mt) cc_final: 0.7832 (tt) REVERT: B 124 ARG cc_start: 0.8225 (ttt-90) cc_final: 0.7854 (ttt-90) REVERT: B 128 LYS cc_start: 0.8083 (mttt) cc_final: 0.7797 (mttt) REVERT: B 132 PHE cc_start: 0.6844 (m-80) cc_final: 0.6009 (m-80) REVERT: A 130 GLU cc_start: 0.8522 (pt0) cc_final: 0.7837 (pp20) REVERT: A 237 ASP cc_start: 0.8054 (m-30) cc_final: 0.7437 (t70) REVERT: A 283 TYR cc_start: 0.7509 (t80) cc_final: 0.7177 (t80) REVERT: A 287 PHE cc_start: 0.7067 (m-80) cc_final: 0.6865 (m-80) REVERT: A 294 ARG cc_start: 0.8121 (mpt-90) cc_final: 0.7867 (mpt-90) REVERT: A 304 MET cc_start: 0.4377 (tpt) cc_final: 0.4147 (tpt) REVERT: A 315 LYS cc_start: 0.7698 (mmtm) cc_final: 0.7367 (mmtm) REVERT: A 332 ASN cc_start: 0.8061 (t0) cc_final: 0.7615 (t0) REVERT: A 337 ARG cc_start: 0.8089 (ttm170) cc_final: 0.7435 (ttp80) REVERT: A 341 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7738 (mt-10) REVERT: A 344 GLN cc_start: 0.8053 (tp-100) cc_final: 0.7701 (pp30) REVERT: A 349 TYR cc_start: 0.7651 (t80) cc_final: 0.7369 (t80) REVERT: A 361 LEU cc_start: 0.7317 (tp) cc_final: 0.6969 (tp) REVERT: A 403 GLU cc_start: 0.7064 (pm20) cc_final: 0.5932 (pm20) REVERT: A 406 GLU cc_start: 0.7412 (tp30) cc_final: 0.7014 (tp30) REVERT: A 407 LEU cc_start: 0.8852 (mt) cc_final: 0.8483 (mt) REVERT: A 410 GLN cc_start: 0.8609 (mm-40) cc_final: 0.7733 (mm-40) REVERT: A 447 GLU cc_start: 0.7781 (mp0) cc_final: 0.7392 (tp30) REVERT: A 449 PHE cc_start: 0.7345 (m-10) cc_final: 0.7105 (m-10) REVERT: A 450 ILE cc_start: 0.8188 (mt) cc_final: 0.7578 (mt) REVERT: A 458 LEU cc_start: 0.7940 (tp) cc_final: 0.7682 (tt) REVERT: A 463 ASP cc_start: 0.6874 (t0) cc_final: 0.6604 (t70) REVERT: A 477 PHE cc_start: 0.7731 (m-80) cc_final: 0.7200 (m-80) REVERT: A 478 MET cc_start: 0.7885 (mtp) cc_final: 0.6521 (mtp) REVERT: A 482 PHE cc_start: 0.7664 (p90) cc_final: 0.7431 (p90) REVERT: A 488 THR cc_start: 0.7105 (m) cc_final: 0.6713 (p) REVERT: A 493 LEU cc_start: 0.7548 (tp) cc_final: 0.6910 (tt) REVERT: A 501 MET cc_start: 0.7485 (mtt) cc_final: 0.6628 (mmt) REVERT: A 502 TYR cc_start: 0.6988 (m-10) cc_final: 0.6717 (m-10) REVERT: A 504 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7097 (mm-30) REVERT: A 505 ARG cc_start: 0.8066 (mtt90) cc_final: 0.7721 (mtt90) REVERT: A 507 ILE cc_start: 0.8339 (mt) cc_final: 0.7927 (mt) REVERT: A 520 ASN cc_start: 0.7089 (t0) cc_final: 0.6611 (m-40) REVERT: A 522 TYR cc_start: 0.8029 (m-80) cc_final: 0.7601 (m-80) REVERT: A 523 LEU cc_start: 0.8585 (tp) cc_final: 0.8136 (tp) REVERT: A 534 ASP cc_start: 0.7681 (m-30) cc_final: 0.7427 (m-30) REVERT: A 540 LEU cc_start: 0.8568 (mm) cc_final: 0.8358 (mm) REVERT: A 542 MET cc_start: 0.7949 (tpp) cc_final: 0.7586 (tpp) REVERT: A 553 LYS cc_start: 0.8720 (mtmt) cc_final: 0.7794 (ptmt) REVERT: A 554 GLN cc_start: 0.7655 (tt0) cc_final: 0.7012 (mm-40) REVERT: A 581 GLU cc_start: 0.7810 (tt0) cc_final: 0.7446 (tt0) REVERT: A 600 TRP cc_start: 0.8196 (t-100) cc_final: 0.7943 (t-100) REVERT: A 617 ILE cc_start: 0.8393 (mm) cc_final: 0.7935 (mm) REVERT: A 621 LEU cc_start: 0.8199 (mm) cc_final: 0.7802 (mp) REVERT: A 635 MET cc_start: 0.7797 (mpp) cc_final: 0.7118 (mpp) REVERT: A 638 TYR cc_start: 0.8037 (m-80) cc_final: 0.6507 (m-80) REVERT: A 658 LEU cc_start: 0.8505 (tp) cc_final: 0.8262 (mt) REVERT: A 660 GLN cc_start: 0.8122 (pp30) cc_final: 0.7863 (pp30) REVERT: A 661 SER cc_start: 0.8321 (m) cc_final: 0.8054 (p) REVERT: A 663 LYS cc_start: 0.7609 (ptmm) cc_final: 0.7053 (ttpp) REVERT: A 708 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8359 (pm20) REVERT: A 711 LYS cc_start: 0.9091 (mmtt) cc_final: 0.8566 (mmtm) REVERT: A 712 GLU cc_start: 0.8548 (tt0) cc_final: 0.8207 (tt0) REVERT: A 720 TYR cc_start: 0.6947 (t80) cc_final: 0.6406 (t80) REVERT: A 726 VAL cc_start: 0.8325 (OUTLIER) cc_final: 0.7987 (t) REVERT: A 727 GLU cc_start: 0.7874 (pt0) cc_final: 0.7416 (pm20) REVERT: A 729 GLN cc_start: 0.8185 (mp10) cc_final: 0.7749 (mp10) REVERT: A 730 PHE cc_start: 0.7459 (t80) cc_final: 0.7191 (t80) REVERT: A 734 ARG cc_start: 0.8484 (ttt-90) cc_final: 0.7725 (ttm-80) REVERT: A 743 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6730 (mp0) REVERT: A 751 ARG cc_start: 0.7257 (mtm-85) cc_final: 0.6927 (mtp85) REVERT: A 753 GLU cc_start: 0.8120 (mp0) cc_final: 0.7788 (mp0) REVERT: A 756 GLU cc_start: 0.7458 (tp30) cc_final: 0.6630 (tp30) REVERT: A 787 ILE cc_start: 0.6650 (OUTLIER) cc_final: 0.6432 (mm) REVERT: A 788 ARG cc_start: 0.7961 (ptp90) cc_final: 0.7450 (ptp90) REVERT: A 789 GLU cc_start: 0.7729 (pt0) cc_final: 0.6933 (mt-10) REVERT: A 805 PHE cc_start: 0.8519 (t80) cc_final: 0.8287 (t80) REVERT: A 820 LEU cc_start: 0.7700 (mm) cc_final: 0.6969 (mm) REVERT: A 822 LYS cc_start: 0.8400 (mptt) cc_final: 0.8097 (mmtm) REVERT: A 862 LEU cc_start: 0.8459 (tt) cc_final: 0.8244 (mt) REVERT: D 21 GLN cc_start: 0.7491 (mt0) cc_final: 0.6866 (mt0) REVERT: D 79 LYS cc_start: 0.8298 (tppt) cc_final: 0.7226 (tppt) REVERT: D 124 ARG cc_start: 0.8168 (ttt-90) cc_final: 0.7843 (ttt-90) REVERT: D 132 PHE cc_start: 0.6801 (m-80) cc_final: 0.6119 (m-80) REVERT: C 129 THR cc_start: 0.8052 (m) cc_final: 0.7634 (p) REVERT: C 131 GLU cc_start: 0.8252 (mp0) cc_final: 0.7729 (mp0) REVERT: C 237 ASP cc_start: 0.7890 (m-30) cc_final: 0.7066 (t70) REVERT: C 241 ARG cc_start: 0.8455 (mtm-85) cc_final: 0.8221 (mtm-85) REVERT: C 283 TYR cc_start: 0.7716 (t80) cc_final: 0.7385 (t80) REVERT: C 287 PHE cc_start: 0.7291 (m-80) cc_final: 0.7070 (m-80) REVERT: C 294 ARG cc_start: 0.8112 (mpt-90) cc_final: 0.7878 (mpt-90) REVERT: C 321 GLN cc_start: 0.8246 (mt0) cc_final: 0.8018 (mm-40) REVERT: C 324 LEU cc_start: 0.8316 (tt) cc_final: 0.8090 (tp) REVERT: C 332 ASN cc_start: 0.7945 (t0) cc_final: 0.7383 (t0) REVERT: C 337 ARG cc_start: 0.8135 (ttm170) cc_final: 0.7497 (ttp80) REVERT: C 349 TYR cc_start: 0.7753 (t80) cc_final: 0.7409 (t80) REVERT: C 382 ASN cc_start: 0.8120 (m-40) cc_final: 0.7891 (m-40) REVERT: C 394 GLU cc_start: 0.6391 (mm-30) cc_final: 0.5398 (mm-30) REVERT: C 403 GLU cc_start: 0.7042 (pm20) cc_final: 0.6003 (pm20) REVERT: C 406 GLU cc_start: 0.7550 (tp30) cc_final: 0.6996 (tp30) REVERT: C 407 LEU cc_start: 0.8812 (mt) cc_final: 0.8473 (mt) REVERT: C 410 GLN cc_start: 0.8537 (mm-40) cc_final: 0.7671 (mm-40) REVERT: C 411 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7481 (mt-10) REVERT: C 447 GLU cc_start: 0.7611 (mp0) cc_final: 0.7128 (tp30) REVERT: C 477 PHE cc_start: 0.7637 (m-80) cc_final: 0.7286 (m-10) REVERT: C 478 MET cc_start: 0.7730 (mtp) cc_final: 0.6907 (mtp) REVERT: C 482 PHE cc_start: 0.7634 (p90) cc_final: 0.7378 (p90) REVERT: C 488 THR cc_start: 0.7213 (m) cc_final: 0.6893 (p) REVERT: C 493 LEU cc_start: 0.7773 (tp) cc_final: 0.7016 (tt) REVERT: C 499 ILE cc_start: 0.7700 (tp) cc_final: 0.7491 (tp) REVERT: C 501 MET cc_start: 0.7400 (mtt) cc_final: 0.7165 (mtt) REVERT: C 504 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7292 (mm-30) REVERT: C 505 ARG cc_start: 0.8059 (mtt90) cc_final: 0.7533 (mtt90) REVERT: C 507 ILE cc_start: 0.8387 (mt) cc_final: 0.7935 (mt) REVERT: C 520 ASN cc_start: 0.7360 (t0) cc_final: 0.7040 (m-40) REVERT: C 522 TYR cc_start: 0.8011 (m-80) cc_final: 0.7720 (m-80) REVERT: C 540 LEU cc_start: 0.8501 (mm) cc_final: 0.8282 (mm) REVERT: C 542 MET cc_start: 0.7984 (tpp) cc_final: 0.7447 (tpp) REVERT: C 546 GLU cc_start: 0.6875 (tt0) cc_final: 0.6317 (tt0) REVERT: C 553 LYS cc_start: 0.8735 (mtmt) cc_final: 0.8166 (ptmt) REVERT: C 555 LEU cc_start: 0.8730 (tp) cc_final: 0.8514 (tp) REVERT: C 589 MET cc_start: 0.6343 (mtp) cc_final: 0.6119 (mtp) REVERT: C 600 TRP cc_start: 0.8253 (t-100) cc_final: 0.7992 (t-100) REVERT: C 617 ILE cc_start: 0.8573 (mm) cc_final: 0.8143 (mm) REVERT: C 621 LEU cc_start: 0.8219 (mm) cc_final: 0.7838 (mt) REVERT: C 635 MET cc_start: 0.7695 (mpp) cc_final: 0.6950 (mpp) REVERT: C 638 TYR cc_start: 0.7934 (m-80) cc_final: 0.6373 (m-80) REVERT: C 651 LEU cc_start: 0.8202 (tp) cc_final: 0.7956 (mt) REVERT: C 658 LEU cc_start: 0.8745 (tp) cc_final: 0.8340 (tp) REVERT: C 661 SER cc_start: 0.8402 (m) cc_final: 0.8008 (p) REVERT: C 682 ILE cc_start: 0.6755 (pt) cc_final: 0.5788 (pt) REVERT: C 711 LYS cc_start: 0.9019 (mmtt) cc_final: 0.8515 (mmtm) REVERT: C 712 GLU cc_start: 0.8649 (tt0) cc_final: 0.8355 (tt0) REVERT: C 720 TYR cc_start: 0.7030 (t80) cc_final: 0.6378 (t80) REVERT: C 726 VAL cc_start: 0.8058 (OUTLIER) cc_final: 0.7672 (t) REVERT: C 729 GLN cc_start: 0.8186 (mp10) cc_final: 0.7879 (mp10) REVERT: C 730 PHE cc_start: 0.7485 (t80) cc_final: 0.7117 (t80) REVERT: C 739 MET cc_start: 0.7184 (ptm) cc_final: 0.6949 (ptm) REVERT: C 743 GLU cc_start: 0.7418 (mm-30) cc_final: 0.7125 (mm-30) REVERT: C 748 TYR cc_start: 0.7149 (t80) cc_final: 0.6854 (t80) REVERT: C 751 ARG cc_start: 0.7315 (mtm-85) cc_final: 0.7052 (mtp85) REVERT: C 753 GLU cc_start: 0.8164 (mp0) cc_final: 0.7905 (mp0) REVERT: C 756 GLU cc_start: 0.7376 (tp30) cc_final: 0.6486 (tp30) REVERT: C 757 LEU cc_start: 0.7371 (mm) cc_final: 0.7147 (mm) REVERT: C 763 ARG cc_start: 0.5179 (mmm160) cc_final: 0.4858 (tpp80) REVERT: C 787 ILE cc_start: 0.6891 (OUTLIER) cc_final: 0.6533 (mm) REVERT: C 788 ARG cc_start: 0.7999 (ptp90) cc_final: 0.7369 (ptp90) REVERT: C 789 GLU cc_start: 0.7881 (pt0) cc_final: 0.7175 (mt-10) REVERT: C 805 PHE cc_start: 0.8475 (t80) cc_final: 0.8244 (t80) REVERT: C 820 LEU cc_start: 0.7518 (mm) cc_final: 0.6792 (mm) REVERT: C 822 LYS cc_start: 0.8473 (mptt) cc_final: 0.8235 (mmtp) REVERT: C 855 LYS cc_start: 0.8803 (tttt) cc_final: 0.7586 (tmtt) outliers start: 10 outliers final: 4 residues processed: 565 average time/residue: 0.3120 time to fit residues: 236.7691 Evaluate side-chains 514 residues out of total 1514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 506 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.3980 chunk 122 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 65 ASN ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 ASN A 285 ASN A 382 ASN A 455 ASN A 515 GLN A 715 ASN D 27 GLN D 65 ASN ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 ASN C 285 ASN C 455 ASN C 515 GLN ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 723 ASN C 738 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13522 Z= 0.222 Angle : 0.674 7.670 18260 Z= 0.359 Chirality : 0.043 0.230 2014 Planarity : 0.006 0.097 2372 Dihedral : 6.132 21.286 1806 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.21 % Allowed : 6.13 % Favored : 93.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.18), residues: 1610 helix: -2.03 (0.15), residues: 832 sheet: -3.14 (0.49), residues: 72 loop : -1.66 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 328 HIS 0.004 0.001 HIS A 655 PHE 0.033 0.002 PHE D 54 TYR 0.028 0.002 TYR C 127 ARG 0.007 0.000 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 1514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 544 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ILE cc_start: 0.8241 (tt) cc_final: 0.7983 (tt) REVERT: B 59 ILE cc_start: 0.7473 (mm) cc_final: 0.7258 (tp) REVERT: B 73 CYS cc_start: 0.7207 (m) cc_final: 0.6839 (m) REVERT: B 88 TYR cc_start: 0.7225 (p90) cc_final: 0.6943 (p90) REVERT: B 108 ILE cc_start: 0.8142 (mt) cc_final: 0.7905 (tt) REVERT: B 128 LYS cc_start: 0.8048 (mttt) cc_final: 0.7715 (mmtt) REVERT: B 132 PHE cc_start: 0.6783 (m-80) cc_final: 0.6017 (m-80) REVERT: A 130 GLU cc_start: 0.8561 (pt0) cc_final: 0.8138 (pt0) REVERT: A 237 ASP cc_start: 0.8301 (m-30) cc_final: 0.7247 (t0) REVERT: A 260 LEU cc_start: 0.9005 (mm) cc_final: 0.8683 (mm) REVERT: A 283 TYR cc_start: 0.7432 (t80) cc_final: 0.7217 (t80) REVERT: A 291 MET cc_start: 0.8243 (ttt) cc_final: 0.7789 (ttt) REVERT: A 304 MET cc_start: 0.4772 (tpt) cc_final: 0.4284 (tpt) REVERT: A 332 ASN cc_start: 0.7822 (t0) cc_final: 0.7223 (t0) REVERT: A 337 ARG cc_start: 0.8050 (ttm170) cc_final: 0.7763 (ttp80) REVERT: A 341 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7713 (pt0) REVERT: A 343 PHE cc_start: 0.8856 (m-80) cc_final: 0.8605 (m-80) REVERT: A 344 GLN cc_start: 0.8078 (tp-100) cc_final: 0.6793 (tp-100) REVERT: A 348 THR cc_start: 0.7737 (m) cc_final: 0.7350 (m) REVERT: A 350 LYS cc_start: 0.7588 (mmpt) cc_final: 0.7370 (mttm) REVERT: A 361 LEU cc_start: 0.7507 (tp) cc_final: 0.7222 (tp) REVERT: A 392 HIS cc_start: 0.7836 (m90) cc_final: 0.7301 (m-70) REVERT: A 403 GLU cc_start: 0.6758 (pm20) cc_final: 0.6226 (pm20) REVERT: A 407 LEU cc_start: 0.8998 (mt) cc_final: 0.8449 (pp) REVERT: A 409 LEU cc_start: 0.8526 (tp) cc_final: 0.8159 (pp) REVERT: A 410 GLN cc_start: 0.8515 (mm-40) cc_final: 0.8253 (mm110) REVERT: A 447 GLU cc_start: 0.7833 (mp0) cc_final: 0.7413 (tp30) REVERT: A 449 PHE cc_start: 0.7222 (m-10) cc_final: 0.6880 (m-10) REVERT: A 450 ILE cc_start: 0.8122 (mt) cc_final: 0.7491 (mt) REVERT: A 458 LEU cc_start: 0.8181 (tp) cc_final: 0.7335 (tt) REVERT: A 463 ASP cc_start: 0.7089 (t0) cc_final: 0.6772 (m-30) REVERT: A 464 TYR cc_start: 0.6822 (t80) cc_final: 0.6322 (t80) REVERT: A 477 PHE cc_start: 0.7810 (m-80) cc_final: 0.7547 (m-80) REVERT: A 478 MET cc_start: 0.7933 (mtp) cc_final: 0.6657 (mtp) REVERT: A 499 ILE cc_start: 0.7801 (tp) cc_final: 0.7252 (tp) REVERT: A 501 MET cc_start: 0.7890 (mtt) cc_final: 0.7186 (ptp) REVERT: A 502 TYR cc_start: 0.6964 (m-10) cc_final: 0.6719 (m-10) REVERT: A 504 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7124 (mm-30) REVERT: A 507 ILE cc_start: 0.8394 (mt) cc_final: 0.7859 (mt) REVERT: A 522 TYR cc_start: 0.7856 (m-80) cc_final: 0.7589 (m-80) REVERT: A 523 LEU cc_start: 0.8458 (tp) cc_final: 0.8248 (tp) REVERT: A 533 ILE cc_start: 0.8302 (pt) cc_final: 0.8073 (pt) REVERT: A 545 MET cc_start: 0.7545 (mtm) cc_final: 0.7153 (mtm) REVERT: A 553 LYS cc_start: 0.8600 (mtmt) cc_final: 0.8042 (ptmt) REVERT: A 572 LYS cc_start: 0.8367 (tttp) cc_final: 0.7860 (ttmm) REVERT: A 573 GLU cc_start: 0.7707 (pp20) cc_final: 0.7309 (pp20) REVERT: A 576 GLN cc_start: 0.7524 (tp-100) cc_final: 0.6855 (tp-100) REVERT: A 577 LEU cc_start: 0.8657 (mt) cc_final: 0.8196 (mt) REVERT: A 593 ASP cc_start: 0.7533 (t0) cc_final: 0.7317 (t0) REVERT: A 605 SER cc_start: 0.7561 (p) cc_final: 0.6641 (p) REVERT: A 613 THR cc_start: 0.8245 (m) cc_final: 0.8043 (m) REVERT: A 617 ILE cc_start: 0.8389 (mm) cc_final: 0.7944 (mm) REVERT: A 621 LEU cc_start: 0.7968 (mm) cc_final: 0.7528 (mp) REVERT: A 635 MET cc_start: 0.7672 (mpp) cc_final: 0.7149 (mpp) REVERT: A 651 LEU cc_start: 0.8469 (mt) cc_final: 0.8142 (mt) REVERT: A 658 LEU cc_start: 0.8318 (tp) cc_final: 0.7804 (tp) REVERT: A 660 GLN cc_start: 0.8061 (pp30) cc_final: 0.7772 (pp30) REVERT: A 661 SER cc_start: 0.8325 (m) cc_final: 0.7926 (p) REVERT: A 663 LYS cc_start: 0.8019 (ptmm) cc_final: 0.7063 (ttpp) REVERT: A 664 ASP cc_start: 0.7781 (m-30) cc_final: 0.6445 (p0) REVERT: A 711 LYS cc_start: 0.9212 (mmtt) cc_final: 0.8726 (mmtm) REVERT: A 712 GLU cc_start: 0.8670 (tt0) cc_final: 0.8347 (tt0) REVERT: A 716 LEU cc_start: 0.8731 (mt) cc_final: 0.8435 (mt) REVERT: A 717 TYR cc_start: 0.7971 (t80) cc_final: 0.7656 (t80) REVERT: A 720 TYR cc_start: 0.7129 (t80) cc_final: 0.6636 (t80) REVERT: A 728 LYS cc_start: 0.8530 (ttpt) cc_final: 0.7670 (ptmm) REVERT: A 729 GLN cc_start: 0.8066 (mp10) cc_final: 0.7347 (mp10) REVERT: A 730 PHE cc_start: 0.7498 (t80) cc_final: 0.7110 (t80) REVERT: A 734 ARG cc_start: 0.8288 (ttt-90) cc_final: 0.7566 (ttt180) REVERT: A 743 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7247 (mm-30) REVERT: A 748 TYR cc_start: 0.6915 (t80) cc_final: 0.6682 (t80) REVERT: A 751 ARG cc_start: 0.7486 (mtm-85) cc_final: 0.7234 (mmm160) REVERT: A 753 GLU cc_start: 0.8298 (mp0) cc_final: 0.7933 (mp0) REVERT: A 756 GLU cc_start: 0.7636 (tp30) cc_final: 0.7158 (tp30) REVERT: A 792 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8232 (mm-30) REVERT: A 805 PHE cc_start: 0.8430 (t80) cc_final: 0.7981 (t80) REVERT: A 806 LEU cc_start: 0.8214 (mt) cc_final: 0.7810 (mt) REVERT: A 822 LYS cc_start: 0.8439 (mptt) cc_final: 0.8106 (mmtm) REVERT: A 862 LEU cc_start: 0.8517 (tt) cc_final: 0.8250 (mt) REVERT: D 21 GLN cc_start: 0.7009 (mt0) cc_final: 0.6805 (mt0) REVERT: D 47 ARG cc_start: 0.7479 (mmm160) cc_final: 0.6425 (mmm160) REVERT: D 65 ASN cc_start: 0.7628 (m-40) cc_final: 0.7383 (m-40) REVERT: D 73 CYS cc_start: 0.7077 (m) cc_final: 0.6707 (m) REVERT: D 79 LYS cc_start: 0.8382 (tppt) cc_final: 0.7249 (tppt) REVERT: D 80 ILE cc_start: 0.8174 (mm) cc_final: 0.7873 (mm) REVERT: D 94 THR cc_start: 0.7345 (p) cc_final: 0.6987 (p) REVERT: D 132 PHE cc_start: 0.6686 (m-80) cc_final: 0.6076 (m-80) REVERT: C 130 GLU cc_start: 0.8510 (pt0) cc_final: 0.8107 (pt0) REVERT: C 260 LEU cc_start: 0.8845 (mm) cc_final: 0.8523 (mm) REVERT: C 291 MET cc_start: 0.8408 (ttt) cc_final: 0.7831 (ptm) REVERT: C 315 LYS cc_start: 0.7875 (mtmm) cc_final: 0.7402 (mttp) REVERT: C 337 ARG cc_start: 0.8105 (ttm170) cc_final: 0.7643 (ttp80) REVERT: C 338 ARG cc_start: 0.8001 (mtp85) cc_final: 0.7458 (mtp-110) REVERT: C 344 GLN cc_start: 0.8035 (tp-100) cc_final: 0.6872 (tp-100) REVERT: C 349 TYR cc_start: 0.7521 (t80) cc_final: 0.7291 (t80) REVERT: C 376 LYS cc_start: 0.8444 (ttmt) cc_final: 0.7240 (tttt) REVERT: C 380 TYR cc_start: 0.8193 (m-10) cc_final: 0.7788 (m-10) REVERT: C 389 ASP cc_start: 0.6353 (t0) cc_final: 0.5931 (t0) REVERT: C 394 GLU cc_start: 0.6351 (mm-30) cc_final: 0.6023 (mm-30) REVERT: C 406 GLU cc_start: 0.7604 (tp30) cc_final: 0.7387 (tt0) REVERT: C 407 LEU cc_start: 0.8956 (mt) cc_final: 0.8321 (pp) REVERT: C 409 LEU cc_start: 0.8532 (tp) cc_final: 0.8078 (pp) REVERT: C 411 GLU cc_start: 0.7778 (mt-10) cc_final: 0.6961 (mt-10) REVERT: C 426 ASP cc_start: 0.8516 (t70) cc_final: 0.8232 (t0) REVERT: C 437 LEU cc_start: 0.7917 (mt) cc_final: 0.7232 (mm) REVERT: C 447 GLU cc_start: 0.7708 (mp0) cc_final: 0.7318 (tp30) REVERT: C 449 PHE cc_start: 0.7341 (m-10) cc_final: 0.7037 (m-10) REVERT: C 450 ILE cc_start: 0.8053 (mt) cc_final: 0.7423 (mt) REVERT: C 459 GLU cc_start: 0.5877 (mp0) cc_final: 0.5671 (mp0) REVERT: C 463 ASP cc_start: 0.7043 (t0) cc_final: 0.5958 (t0) REVERT: C 477 PHE cc_start: 0.7699 (m-80) cc_final: 0.7048 (m-80) REVERT: C 478 MET cc_start: 0.7752 (mtp) cc_final: 0.6681 (mtp) REVERT: C 493 LEU cc_start: 0.7426 (tp) cc_final: 0.6939 (tp) REVERT: C 499 ILE cc_start: 0.7965 (tp) cc_final: 0.7696 (tp) REVERT: C 501 MET cc_start: 0.7862 (mtt) cc_final: 0.7397 (mtt) REVERT: C 502 TYR cc_start: 0.7018 (m-10) cc_final: 0.6747 (m-10) REVERT: C 504 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7267 (mm-30) REVERT: C 505 ARG cc_start: 0.8098 (mtt90) cc_final: 0.7406 (mtt90) REVERT: C 507 ILE cc_start: 0.8378 (mt) cc_final: 0.7898 (mt) REVERT: C 522 TYR cc_start: 0.7818 (m-80) cc_final: 0.7584 (m-80) REVERT: C 542 MET cc_start: 0.7636 (tpp) cc_final: 0.7119 (tpp) REVERT: C 545 MET cc_start: 0.7506 (mtm) cc_final: 0.6902 (mtm) REVERT: C 576 GLN cc_start: 0.7005 (tm-30) cc_final: 0.6405 (tm-30) REVERT: C 577 LEU cc_start: 0.8597 (mt) cc_final: 0.8118 (mt) REVERT: C 619 LEU cc_start: 0.8561 (tp) cc_final: 0.8338 (tp) REVERT: C 621 LEU cc_start: 0.8090 (mm) cc_final: 0.7646 (mm) REVERT: C 625 ASN cc_start: 0.7974 (m110) cc_final: 0.7643 (m110) REVERT: C 626 ASN cc_start: 0.7843 (m-40) cc_final: 0.7499 (m110) REVERT: C 635 MET cc_start: 0.7547 (mpp) cc_final: 0.6796 (mpp) REVERT: C 641 LEU cc_start: 0.8262 (mt) cc_final: 0.7881 (mt) REVERT: C 648 PHE cc_start: 0.8663 (p90) cc_final: 0.8201 (p90) REVERT: C 658 LEU cc_start: 0.8453 (tp) cc_final: 0.7930 (tp) REVERT: C 663 LYS cc_start: 0.8148 (ptmm) cc_final: 0.6967 (mmtt) REVERT: C 664 ASP cc_start: 0.7972 (m-30) cc_final: 0.6327 (p0) REVERT: C 711 LYS cc_start: 0.9168 (mmtt) cc_final: 0.8643 (mmtm) REVERT: C 712 GLU cc_start: 0.8763 (tt0) cc_final: 0.8405 (tt0) REVERT: C 716 LEU cc_start: 0.8736 (mt) cc_final: 0.8418 (mp) REVERT: C 720 TYR cc_start: 0.7181 (t80) cc_final: 0.6585 (t80) REVERT: C 738 HIS cc_start: 0.7873 (t-90) cc_final: 0.6983 (t-90) REVERT: C 743 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7494 (mm-30) REVERT: C 748 TYR cc_start: 0.6924 (t80) cc_final: 0.6525 (t80) REVERT: C 756 GLU cc_start: 0.7519 (tp30) cc_final: 0.6918 (tp30) REVERT: C 789 GLU cc_start: 0.7977 (pt0) cc_final: 0.7403 (mt-10) REVERT: C 791 TRP cc_start: 0.7579 (t60) cc_final: 0.7163 (t60) REVERT: C 801 GLN cc_start: 0.8202 (mp10) cc_final: 0.7896 (mp10) REVERT: C 822 LYS cc_start: 0.8513 (mptt) cc_final: 0.8264 (mmtm) REVERT: C 855 LYS cc_start: 0.8884 (tttt) cc_final: 0.7865 (tppt) outliers start: 3 outliers final: 0 residues processed: 547 average time/residue: 0.3175 time to fit residues: 232.4786 Evaluate side-chains 520 residues out of total 1514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 520 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 122 optimal weight: 0.3980 chunk 100 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 147 optimal weight: 0.4980 chunk 159 optimal weight: 7.9990 chunk 131 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 50 optimal weight: 0.0370 chunk 118 optimal weight: 3.9990 overall best weight: 0.7862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN A 518 GLN A 626 ASN D 134 ASN ** C 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 ASN C 520 ASN C 723 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13522 Z= 0.192 Angle : 0.640 12.947 18260 Z= 0.330 Chirality : 0.043 0.168 2014 Planarity : 0.005 0.092 2372 Dihedral : 5.489 19.061 1806 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.07 % Allowed : 5.37 % Favored : 94.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.19), residues: 1610 helix: -1.22 (0.17), residues: 808 sheet: -3.16 (0.50), residues: 72 loop : -1.35 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 139 HIS 0.003 0.001 HIS A 655 PHE 0.030 0.002 PHE A 790 TYR 0.017 0.001 TYR A 134 ARG 0.005 0.000 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 1514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 518 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 LEU cc_start: 0.8124 (mm) cc_final: 0.7853 (mm) REVERT: B 73 CYS cc_start: 0.7182 (m) cc_final: 0.6883 (m) REVERT: B 77 TYR cc_start: 0.8021 (m-80) cc_final: 0.7501 (m-80) REVERT: B 82 GLU cc_start: 0.8111 (tt0) cc_final: 0.7897 (tt0) REVERT: B 108 ILE cc_start: 0.8045 (mt) cc_final: 0.7779 (tt) REVERT: B 114 GLN cc_start: 0.7215 (mp10) cc_final: 0.6912 (mp10) REVERT: B 124 ARG cc_start: 0.8263 (ttt-90) cc_final: 0.7912 (ttt-90) REVERT: B 128 LYS cc_start: 0.8136 (mttt) cc_final: 0.7930 (mttt) REVERT: B 132 PHE cc_start: 0.6967 (m-80) cc_final: 0.6160 (m-80) REVERT: A 130 GLU cc_start: 0.8512 (pt0) cc_final: 0.7579 (pm20) REVERT: A 138 GLU cc_start: 0.8319 (mp0) cc_final: 0.7861 (mp0) REVERT: A 237 ASP cc_start: 0.8450 (m-30) cc_final: 0.7820 (t0) REVERT: A 241 ARG cc_start: 0.8704 (mtp-110) cc_final: 0.8449 (mtp-110) REVERT: A 287 PHE cc_start: 0.6820 (m-80) cc_final: 0.6540 (m-80) REVERT: A 291 MET cc_start: 0.8400 (ttt) cc_final: 0.7828 (ttp) REVERT: A 294 ARG cc_start: 0.8289 (mpt180) cc_final: 0.7865 (mpt180) REVERT: A 304 MET cc_start: 0.4665 (tpt) cc_final: 0.3823 (tpt) REVERT: A 332 ASN cc_start: 0.7871 (t0) cc_final: 0.7168 (t0) REVERT: A 337 ARG cc_start: 0.8090 (ttm170) cc_final: 0.7238 (ttp80) REVERT: A 338 ARG cc_start: 0.8003 (mtp85) cc_final: 0.7761 (mmm-85) REVERT: A 341 GLU cc_start: 0.8140 (mt-10) cc_final: 0.6808 (mt-10) REVERT: A 344 GLN cc_start: 0.8072 (tp-100) cc_final: 0.6823 (tp-100) REVERT: A 345 GLN cc_start: 0.8282 (mt0) cc_final: 0.7424 (tp40) REVERT: A 346 LEU cc_start: 0.8567 (tp) cc_final: 0.8348 (tp) REVERT: A 361 LEU cc_start: 0.7501 (tp) cc_final: 0.7124 (tp) REVERT: A 392 HIS cc_start: 0.7834 (m90) cc_final: 0.7411 (m90) REVERT: A 406 GLU cc_start: 0.7648 (tt0) cc_final: 0.7334 (tt0) REVERT: A 407 LEU cc_start: 0.8954 (mt) cc_final: 0.8531 (pp) REVERT: A 408 THR cc_start: 0.8255 (m) cc_final: 0.8026 (m) REVERT: A 437 LEU cc_start: 0.8090 (mm) cc_final: 0.7679 (tt) REVERT: A 447 GLU cc_start: 0.7860 (mp0) cc_final: 0.7473 (tp30) REVERT: A 450 ILE cc_start: 0.8137 (mt) cc_final: 0.7387 (mt) REVERT: A 463 ASP cc_start: 0.7238 (t0) cc_final: 0.6367 (t70) REVERT: A 464 TYR cc_start: 0.6694 (t80) cc_final: 0.6157 (t80) REVERT: A 477 PHE cc_start: 0.7903 (m-80) cc_final: 0.7612 (m-80) REVERT: A 478 MET cc_start: 0.7884 (mtp) cc_final: 0.6365 (mtp) REVERT: A 489 LYS cc_start: 0.8021 (mtmm) cc_final: 0.7784 (ptpp) REVERT: A 499 ILE cc_start: 0.7814 (tp) cc_final: 0.7428 (tp) REVERT: A 502 TYR cc_start: 0.7013 (m-10) cc_final: 0.6787 (m-10) REVERT: A 504 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7225 (mm-30) REVERT: A 505 ARG cc_start: 0.8206 (mtt90) cc_final: 0.7609 (mtt90) REVERT: A 507 ILE cc_start: 0.8437 (mt) cc_final: 0.7813 (mp) REVERT: A 520 ASN cc_start: 0.6998 (t0) cc_final: 0.6783 (m-40) REVERT: A 522 TYR cc_start: 0.7964 (m-80) cc_final: 0.7385 (m-80) REVERT: A 533 ILE cc_start: 0.8227 (pt) cc_final: 0.7982 (pt) REVERT: A 534 ASP cc_start: 0.7654 (m-30) cc_final: 0.7393 (m-30) REVERT: A 543 ILE cc_start: 0.8699 (mt) cc_final: 0.7680 (mt) REVERT: A 545 MET cc_start: 0.7629 (mtm) cc_final: 0.7185 (mtm) REVERT: A 550 ASP cc_start: 0.7603 (p0) cc_final: 0.7214 (p0) REVERT: A 554 GLN cc_start: 0.7517 (mm-40) cc_final: 0.6902 (tp40) REVERT: A 572 LYS cc_start: 0.8266 (tttp) cc_final: 0.7766 (ttmm) REVERT: A 573 GLU cc_start: 0.7634 (pp20) cc_final: 0.7280 (pp20) REVERT: A 589 MET cc_start: 0.5763 (mtt) cc_final: 0.3986 (mtt) REVERT: A 593 ASP cc_start: 0.7499 (t0) cc_final: 0.7224 (t0) REVERT: A 605 SER cc_start: 0.7450 (p) cc_final: 0.6555 (p) REVERT: A 617 ILE cc_start: 0.8395 (mm) cc_final: 0.7967 (mm) REVERT: A 621 LEU cc_start: 0.7909 (mm) cc_final: 0.7331 (mt) REVERT: A 625 ASN cc_start: 0.8038 (m110) cc_final: 0.7735 (m110) REVERT: A 635 MET cc_start: 0.7747 (mpp) cc_final: 0.7197 (mpp) REVERT: A 642 MET cc_start: 0.7810 (mmp) cc_final: 0.7573 (mmp) REVERT: A 651 LEU cc_start: 0.8467 (mt) cc_final: 0.8198 (mt) REVERT: A 658 LEU cc_start: 0.8211 (tp) cc_final: 0.7906 (tp) REVERT: A 660 GLN cc_start: 0.8036 (pp30) cc_final: 0.7522 (pp30) REVERT: A 663 LYS cc_start: 0.7592 (ptmm) cc_final: 0.7378 (ttpp) REVERT: A 682 ILE cc_start: 0.8676 (tp) cc_final: 0.7981 (tp) REVERT: A 711 LYS cc_start: 0.9258 (mmtt) cc_final: 0.8774 (mmtm) REVERT: A 717 TYR cc_start: 0.8213 (t80) cc_final: 0.7888 (t80) REVERT: A 720 TYR cc_start: 0.7289 (t80) cc_final: 0.6775 (t80) REVERT: A 727 GLU cc_start: 0.7710 (pm20) cc_final: 0.7346 (pm20) REVERT: A 728 LYS cc_start: 0.8423 (ttpt) cc_final: 0.7430 (ptmm) REVERT: A 729 GLN cc_start: 0.7978 (mp10) cc_final: 0.7164 (mp10) REVERT: A 730 PHE cc_start: 0.7474 (t80) cc_final: 0.7140 (t80) REVERT: A 734 ARG cc_start: 0.8163 (ttt-90) cc_final: 0.7285 (ttm-80) REVERT: A 743 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7377 (mm-30) REVERT: A 748 TYR cc_start: 0.6822 (t80) cc_final: 0.6601 (t80) REVERT: A 753 GLU cc_start: 0.8300 (mp0) cc_final: 0.7979 (mp0) REVERT: A 792 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8149 (mm-30) REVERT: A 822 LYS cc_start: 0.8443 (mptt) cc_final: 0.8191 (mmtm) REVERT: A 862 LEU cc_start: 0.8505 (tt) cc_final: 0.8222 (mt) REVERT: D 22 LEU cc_start: 0.8159 (mm) cc_final: 0.7874 (mm) REVERT: D 47 ARG cc_start: 0.7536 (mmm160) cc_final: 0.6537 (mmm160) REVERT: D 65 ASN cc_start: 0.7607 (m-40) cc_final: 0.7310 (m-40) REVERT: D 73 CYS cc_start: 0.7001 (m) cc_final: 0.6585 (m) REVERT: D 124 ARG cc_start: 0.8206 (ttt-90) cc_final: 0.7877 (ttt-90) REVERT: D 132 PHE cc_start: 0.6813 (m-80) cc_final: 0.6109 (m-80) REVERT: D 134 ASN cc_start: 0.7181 (t0) cc_final: 0.6505 (t0) REVERT: D 138 ARG cc_start: 0.6788 (ptt-90) cc_final: 0.6413 (ptt-90) REVERT: C 130 GLU cc_start: 0.8468 (pt0) cc_final: 0.8058 (pt0) REVERT: C 237 ASP cc_start: 0.8109 (m-30) cc_final: 0.7623 (t0) REVERT: C 283 TYR cc_start: 0.7932 (t80) cc_final: 0.6857 (t80) REVERT: C 288 ILE cc_start: 0.8580 (tt) cc_final: 0.8141 (tt) REVERT: C 291 MET cc_start: 0.8352 (ttt) cc_final: 0.8103 (ptm) REVERT: C 315 LYS cc_start: 0.7830 (mtmm) cc_final: 0.7030 (mttt) REVERT: C 337 ARG cc_start: 0.8061 (ttm170) cc_final: 0.7697 (ttp80) REVERT: C 344 GLN cc_start: 0.8055 (tp-100) cc_final: 0.6961 (tp-100) REVERT: C 349 TYR cc_start: 0.7579 (t80) cc_final: 0.7274 (t80) REVERT: C 376 LYS cc_start: 0.8742 (ttpt) cc_final: 0.7384 (tttt) REVERT: C 380 TYR cc_start: 0.8105 (m-10) cc_final: 0.7625 (m-10) REVERT: C 407 LEU cc_start: 0.8939 (mt) cc_final: 0.8717 (mt) REVERT: C 411 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7160 (mt-10) REVERT: C 447 GLU cc_start: 0.7763 (mp0) cc_final: 0.7350 (tp30) REVERT: C 450 ILE cc_start: 0.8148 (mt) cc_final: 0.7396 (mt) REVERT: C 477 PHE cc_start: 0.7729 (m-80) cc_final: 0.7416 (m-80) REVERT: C 478 MET cc_start: 0.7689 (mtp) cc_final: 0.6508 (mtp) REVERT: C 493 LEU cc_start: 0.7403 (tp) cc_final: 0.6955 (tp) REVERT: C 496 ASP cc_start: 0.7241 (t0) cc_final: 0.6449 (t70) REVERT: C 497 ASN cc_start: 0.7537 (m110) cc_final: 0.7252 (m-40) REVERT: C 499 ILE cc_start: 0.7995 (tp) cc_final: 0.7656 (tp) REVERT: C 502 TYR cc_start: 0.7056 (m-10) cc_final: 0.6786 (m-10) REVERT: C 504 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7382 (mm-30) REVERT: C 505 ARG cc_start: 0.8092 (mtt90) cc_final: 0.7422 (mtt90) REVERT: C 507 ILE cc_start: 0.8341 (mt) cc_final: 0.7716 (mp) REVERT: C 520 ASN cc_start: 0.7593 (t0) cc_final: 0.7246 (p0) REVERT: C 522 TYR cc_start: 0.7767 (m-80) cc_final: 0.7330 (m-80) REVERT: C 540 LEU cc_start: 0.8560 (mm) cc_final: 0.8354 (mm) REVERT: C 542 MET cc_start: 0.7687 (tpp) cc_final: 0.7141 (tpp) REVERT: C 543 ILE cc_start: 0.8745 (mt) cc_final: 0.8316 (mt) REVERT: C 545 MET cc_start: 0.7624 (mtm) cc_final: 0.7093 (mtm) REVERT: C 555 LEU cc_start: 0.8506 (tp) cc_final: 0.8175 (tp) REVERT: C 573 GLU cc_start: 0.7611 (pp20) cc_final: 0.7234 (pp20) REVERT: C 576 GLN cc_start: 0.7058 (tm-30) cc_final: 0.6503 (tm-30) REVERT: C 577 LEU cc_start: 0.8561 (mt) cc_final: 0.8055 (mt) REVERT: C 617 ILE cc_start: 0.8550 (mm) cc_final: 0.8323 (mm) REVERT: C 619 LEU cc_start: 0.8615 (tp) cc_final: 0.8406 (tp) REVERT: C 621 LEU cc_start: 0.7940 (mm) cc_final: 0.7523 (mm) REVERT: C 625 ASN cc_start: 0.8059 (m110) cc_final: 0.7826 (m110) REVERT: C 626 ASN cc_start: 0.7947 (m-40) cc_final: 0.7629 (m110) REVERT: C 635 MET cc_start: 0.7691 (mpp) cc_final: 0.7187 (mpp) REVERT: C 641 LEU cc_start: 0.8239 (mt) cc_final: 0.8002 (pp) REVERT: C 651 LEU cc_start: 0.8405 (mt) cc_final: 0.8109 (mp) REVERT: C 658 LEU cc_start: 0.8208 (tp) cc_final: 0.7977 (tp) REVERT: C 659 TYR cc_start: 0.8640 (t80) cc_final: 0.8362 (t80) REVERT: C 661 SER cc_start: 0.8356 (p) cc_final: 0.8039 (p) REVERT: C 663 LYS cc_start: 0.8171 (ptmm) cc_final: 0.7470 (ttpp) REVERT: C 667 GLU cc_start: 0.7923 (pp20) cc_final: 0.7661 (pp20) REVERT: C 682 ILE cc_start: 0.8345 (tp) cc_final: 0.7891 (tp) REVERT: C 711 LYS cc_start: 0.9229 (mmtt) cc_final: 0.8708 (mmtm) REVERT: C 712 GLU cc_start: 0.8736 (tt0) cc_final: 0.7966 (tt0) REVERT: C 716 LEU cc_start: 0.8751 (mt) cc_final: 0.8366 (mp) REVERT: C 717 TYR cc_start: 0.8296 (t80) cc_final: 0.7978 (t80) REVERT: C 720 TYR cc_start: 0.7396 (t80) cc_final: 0.6846 (t80) REVERT: C 730 PHE cc_start: 0.7475 (t80) cc_final: 0.7193 (t80) REVERT: C 738 HIS cc_start: 0.7590 (t-90) cc_final: 0.7211 (t-90) REVERT: C 743 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7697 (mm-30) REVERT: C 748 TYR cc_start: 0.6845 (t80) cc_final: 0.6556 (t80) REVERT: C 750 PHE cc_start: 0.7715 (m-80) cc_final: 0.7457 (m-10) REVERT: C 754 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7679 (mp0) REVERT: C 801 GLN cc_start: 0.8258 (mp10) cc_final: 0.8018 (mp10) outliers start: 1 outliers final: 1 residues processed: 518 average time/residue: 0.3216 time to fit residues: 222.7871 Evaluate side-chains 500 residues out of total 1514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 499 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 16 optimal weight: 0.0000 chunk 70 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 147 optimal weight: 0.9980 chunk 156 optimal weight: 5.9990 chunk 77 optimal weight: 0.2980 chunk 140 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN A 520 ASN A 576 GLN ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN ** D 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 ASN ** C 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 ASN ** C 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 723 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13522 Z= 0.170 Angle : 0.602 9.788 18260 Z= 0.309 Chirality : 0.042 0.205 2014 Planarity : 0.004 0.052 2372 Dihedral : 5.163 23.109 1806 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.20), residues: 1610 helix: -0.77 (0.18), residues: 808 sheet: -3.02 (0.53), residues: 72 loop : -1.17 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP A 328 HIS 0.002 0.001 HIS A 655 PHE 0.023 0.002 PHE A 790 TYR 0.019 0.001 TYR C 717 ARG 0.006 0.000 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 1514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 522 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 LEU cc_start: 0.8091 (mm) cc_final: 0.7878 (mm) REVERT: B 73 CYS cc_start: 0.7173 (m) cc_final: 0.6954 (m) REVERT: B 77 TYR cc_start: 0.8008 (m-80) cc_final: 0.7477 (m-80) REVERT: B 82 GLU cc_start: 0.8162 (tt0) cc_final: 0.7920 (tt0) REVERT: B 108 ILE cc_start: 0.8043 (mt) cc_final: 0.7792 (tt) REVERT: B 114 GLN cc_start: 0.7145 (mp10) cc_final: 0.6865 (mp10) REVERT: B 132 PHE cc_start: 0.7030 (m-80) cc_final: 0.6257 (m-80) REVERT: A 130 GLU cc_start: 0.8465 (pt0) cc_final: 0.7442 (pm20) REVERT: A 237 ASP cc_start: 0.8422 (m-30) cc_final: 0.7769 (t0) REVERT: A 241 ARG cc_start: 0.8704 (mtp-110) cc_final: 0.8442 (mtp-110) REVERT: A 251 LYS cc_start: 0.8438 (mttp) cc_final: 0.8097 (tptp) REVERT: A 287 PHE cc_start: 0.6844 (m-80) cc_final: 0.6565 (m-80) REVERT: A 297 HIS cc_start: 0.7810 (t70) cc_final: 0.7592 (t70) REVERT: A 304 MET cc_start: 0.4561 (tpt) cc_final: 0.3870 (tpt) REVERT: A 315 LYS cc_start: 0.7961 (mmtm) cc_final: 0.7490 (mmtm) REVERT: A 326 ARG cc_start: 0.7750 (mtm-85) cc_final: 0.7504 (mtm-85) REVERT: A 332 ASN cc_start: 0.7877 (t0) cc_final: 0.7264 (t0) REVERT: A 337 ARG cc_start: 0.8070 (ttm170) cc_final: 0.7221 (ttp80) REVERT: A 338 ARG cc_start: 0.8078 (mtp85) cc_final: 0.7527 (mmm-85) REVERT: A 341 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7273 (mt-10) REVERT: A 344 GLN cc_start: 0.8054 (tp-100) cc_final: 0.6698 (tp-100) REVERT: A 345 GLN cc_start: 0.8199 (mt0) cc_final: 0.7993 (mt0) REVERT: A 361 LEU cc_start: 0.7420 (tp) cc_final: 0.7048 (tp) REVERT: A 373 LYS cc_start: 0.8051 (mtpp) cc_final: 0.7847 (mtpp) REVERT: A 392 HIS cc_start: 0.7816 (m90) cc_final: 0.7391 (m90) REVERT: A 394 GLU cc_start: 0.6431 (mm-30) cc_final: 0.5233 (mm-30) REVERT: A 407 LEU cc_start: 0.8856 (mt) cc_final: 0.8404 (pp) REVERT: A 408 THR cc_start: 0.8154 (m) cc_final: 0.7283 (m) REVERT: A 411 GLU cc_start: 0.7707 (mt-10) cc_final: 0.6948 (mt-10) REVERT: A 420 LYS cc_start: 0.7724 (pttm) cc_final: 0.7516 (ptmm) REVERT: A 447 GLU cc_start: 0.7879 (mp0) cc_final: 0.7564 (tp30) REVERT: A 450 ILE cc_start: 0.8044 (mt) cc_final: 0.7274 (mt) REVERT: A 458 LEU cc_start: 0.8272 (tt) cc_final: 0.7958 (tp) REVERT: A 463 ASP cc_start: 0.7258 (t0) cc_final: 0.6353 (t70) REVERT: A 464 TYR cc_start: 0.6648 (t80) cc_final: 0.6106 (t80) REVERT: A 477 PHE cc_start: 0.7788 (m-80) cc_final: 0.7558 (m-80) REVERT: A 478 MET cc_start: 0.7901 (mtp) cc_final: 0.6289 (mtp) REVERT: A 489 LYS cc_start: 0.7946 (mtmm) cc_final: 0.7665 (ptpp) REVERT: A 499 ILE cc_start: 0.7823 (tp) cc_final: 0.7454 (tp) REVERT: A 504 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7275 (mm-30) REVERT: A 505 ARG cc_start: 0.8155 (mtt90) cc_final: 0.7671 (mtt90) REVERT: A 507 ILE cc_start: 0.8416 (mt) cc_final: 0.7786 (mp) REVERT: A 515 GLN cc_start: 0.7916 (mm110) cc_final: 0.7678 (tm-30) REVERT: A 520 ASN cc_start: 0.7312 (t0) cc_final: 0.6981 (p0) REVERT: A 522 TYR cc_start: 0.7869 (m-80) cc_final: 0.7280 (m-80) REVERT: A 532 ILE cc_start: 0.7910 (pt) cc_final: 0.7214 (pt) REVERT: A 543 ILE cc_start: 0.8671 (mt) cc_final: 0.7837 (mt) REVERT: A 545 MET cc_start: 0.7597 (mtm) cc_final: 0.7135 (mtm) REVERT: A 550 ASP cc_start: 0.7281 (p0) cc_final: 0.6909 (p0) REVERT: A 551 LEU cc_start: 0.8866 (mp) cc_final: 0.8653 (mp) REVERT: A 572 LYS cc_start: 0.8100 (tptt) cc_final: 0.7332 (tptp) REVERT: A 573 GLU cc_start: 0.7549 (pp20) cc_final: 0.7306 (pp20) REVERT: A 593 ASP cc_start: 0.7523 (t0) cc_final: 0.7181 (t70) REVERT: A 605 SER cc_start: 0.7432 (p) cc_final: 0.6526 (p) REVERT: A 611 GLN cc_start: 0.7432 (tm-30) cc_final: 0.6488 (tm-30) REVERT: A 617 ILE cc_start: 0.8394 (mm) cc_final: 0.8038 (mm) REVERT: A 621 LEU cc_start: 0.7896 (mm) cc_final: 0.7396 (mp) REVERT: A 635 MET cc_start: 0.7565 (mpp) cc_final: 0.7098 (mpp) REVERT: A 642 MET cc_start: 0.7890 (mmp) cc_final: 0.7647 (mmp) REVERT: A 651 LEU cc_start: 0.8447 (mt) cc_final: 0.8155 (mt) REVERT: A 658 LEU cc_start: 0.8176 (tp) cc_final: 0.7786 (tp) REVERT: A 660 GLN cc_start: 0.7951 (pp30) cc_final: 0.7359 (pp30) REVERT: A 661 SER cc_start: 0.8475 (m) cc_final: 0.7987 (m) REVERT: A 663 LYS cc_start: 0.7993 (ptmm) cc_final: 0.7461 (ttpp) REVERT: A 682 ILE cc_start: 0.8709 (tp) cc_final: 0.8278 (tp) REVERT: A 711 LYS cc_start: 0.9258 (mmtt) cc_final: 0.8787 (mmtm) REVERT: A 720 TYR cc_start: 0.7297 (t80) cc_final: 0.6721 (t80) REVERT: A 727 GLU cc_start: 0.7669 (pm20) cc_final: 0.7279 (pm20) REVERT: A 728 LYS cc_start: 0.8376 (ttpt) cc_final: 0.7382 (ptmm) REVERT: A 729 GLN cc_start: 0.7853 (mp10) cc_final: 0.6939 (mp10) REVERT: A 730 PHE cc_start: 0.7470 (t80) cc_final: 0.7188 (t80) REVERT: A 734 ARG cc_start: 0.8078 (ttt-90) cc_final: 0.7580 (ttm-80) REVERT: A 739 MET cc_start: 0.7358 (ptm) cc_final: 0.7125 (ptm) REVERT: A 743 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7380 (mm-30) REVERT: A 750 PHE cc_start: 0.7741 (m-80) cc_final: 0.7426 (m-10) REVERT: A 753 GLU cc_start: 0.8307 (mp0) cc_final: 0.7934 (mp0) REVERT: A 756 GLU cc_start: 0.7400 (tp30) cc_final: 0.6961 (tp30) REVERT: A 780 TYR cc_start: 0.6152 (t80) cc_final: 0.4685 (t80) REVERT: A 792 GLU cc_start: 0.8482 (mm-30) cc_final: 0.7799 (mm-30) REVERT: A 822 LYS cc_start: 0.8457 (mptt) cc_final: 0.8176 (mmtm) REVERT: D 22 LEU cc_start: 0.8182 (mm) cc_final: 0.7975 (mm) REVERT: D 47 ARG cc_start: 0.7497 (mmm160) cc_final: 0.6572 (mmm160) REVERT: D 65 ASN cc_start: 0.7541 (m-40) cc_final: 0.7275 (m-40) REVERT: D 73 CYS cc_start: 0.6631 (m) cc_final: 0.6270 (m) REVERT: D 88 TYR cc_start: 0.7105 (p90) cc_final: 0.6846 (p90) REVERT: D 114 GLN cc_start: 0.6827 (mp10) cc_final: 0.6616 (mp10) REVERT: D 132 PHE cc_start: 0.6840 (m-80) cc_final: 0.6115 (m-80) REVERT: D 138 ARG cc_start: 0.6632 (ptt-90) cc_final: 0.6093 (ptt-90) REVERT: C 237 ASP cc_start: 0.8079 (m-30) cc_final: 0.7662 (t0) REVERT: C 288 ILE cc_start: 0.8603 (tt) cc_final: 0.6801 (tt) REVERT: C 291 MET cc_start: 0.8390 (ttt) cc_final: 0.8052 (ptt) REVERT: C 304 MET cc_start: 0.4932 (tpt) cc_final: 0.4632 (tpt) REVERT: C 315 LYS cc_start: 0.7860 (mtmm) cc_final: 0.7047 (mttt) REVERT: C 330 LYS cc_start: 0.8501 (mmmt) cc_final: 0.8174 (mmtm) REVERT: C 337 ARG cc_start: 0.8038 (ttm170) cc_final: 0.7580 (ttp80) REVERT: C 344 GLN cc_start: 0.8084 (tp-100) cc_final: 0.7075 (tp-100) REVERT: C 349 TYR cc_start: 0.7592 (t80) cc_final: 0.7311 (t80) REVERT: C 376 LYS cc_start: 0.8706 (ttpt) cc_final: 0.7211 (tttt) REVERT: C 380 TYR cc_start: 0.7946 (m-10) cc_final: 0.7590 (m-10) REVERT: C 407 LEU cc_start: 0.8939 (mt) cc_final: 0.8341 (pp) REVERT: C 408 THR cc_start: 0.8244 (m) cc_final: 0.7389 (m) REVERT: C 411 GLU cc_start: 0.7717 (mt-10) cc_final: 0.6809 (mt-10) REVERT: C 447 GLU cc_start: 0.7718 (mp0) cc_final: 0.7398 (tp30) REVERT: C 450 ILE cc_start: 0.7992 (mt) cc_final: 0.7388 (mt) REVERT: C 463 ASP cc_start: 0.7183 (m-30) cc_final: 0.6941 (m-30) REVERT: C 477 PHE cc_start: 0.7656 (m-80) cc_final: 0.7163 (m-80) REVERT: C 478 MET cc_start: 0.7785 (mtp) cc_final: 0.7165 (mtp) REVERT: C 499 ILE cc_start: 0.7962 (tp) cc_final: 0.7601 (tp) REVERT: C 502 TYR cc_start: 0.6980 (m-10) cc_final: 0.6739 (m-10) REVERT: C 504 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7424 (mm-30) REVERT: C 505 ARG cc_start: 0.8043 (mtt90) cc_final: 0.7421 (mtt90) REVERT: C 507 ILE cc_start: 0.8358 (mt) cc_final: 0.7817 (mp) REVERT: C 522 TYR cc_start: 0.7722 (m-80) cc_final: 0.7331 (m-80) REVERT: C 539 ARG cc_start: 0.7931 (tpp80) cc_final: 0.7728 (ttm-80) REVERT: C 540 LEU cc_start: 0.8642 (mm) cc_final: 0.8404 (mm) REVERT: C 542 MET cc_start: 0.7676 (tpp) cc_final: 0.7072 (tpp) REVERT: C 545 MET cc_start: 0.7634 (mtm) cc_final: 0.7097 (mtm) REVERT: C 555 LEU cc_start: 0.8567 (tp) cc_final: 0.8185 (tp) REVERT: C 576 GLN cc_start: 0.6980 (tm-30) cc_final: 0.6397 (tm-30) REVERT: C 577 LEU cc_start: 0.8521 (mt) cc_final: 0.8174 (mt) REVERT: C 581 GLU cc_start: 0.7610 (pp20) cc_final: 0.7325 (pp20) REVERT: C 617 ILE cc_start: 0.8513 (mm) cc_final: 0.8307 (mm) REVERT: C 619 LEU cc_start: 0.8597 (tp) cc_final: 0.8392 (tp) REVERT: C 621 LEU cc_start: 0.8015 (mm) cc_final: 0.7622 (mm) REVERT: C 625 ASN cc_start: 0.8274 (m110) cc_final: 0.7843 (m110) REVERT: C 626 ASN cc_start: 0.7998 (m-40) cc_final: 0.7639 (m110) REVERT: C 635 MET cc_start: 0.7701 (mpp) cc_final: 0.7092 (mpp) REVERT: C 640 LYS cc_start: 0.7747 (mtpp) cc_final: 0.7091 (ttmm) REVERT: C 641 LEU cc_start: 0.8548 (mt) cc_final: 0.8079 (mm) REVERT: C 648 PHE cc_start: 0.8622 (p90) cc_final: 0.8072 (p90) REVERT: C 651 LEU cc_start: 0.8450 (mt) cc_final: 0.7965 (mt) REVERT: C 658 LEU cc_start: 0.8232 (tp) cc_final: 0.7930 (tp) REVERT: C 659 TYR cc_start: 0.8710 (t80) cc_final: 0.8236 (t80) REVERT: C 660 GLN cc_start: 0.8463 (mm-40) cc_final: 0.7997 (mm-40) REVERT: C 663 LYS cc_start: 0.7844 (ptmm) cc_final: 0.7384 (mmtt) REVERT: C 667 GLU cc_start: 0.7911 (pp20) cc_final: 0.7690 (pp20) REVERT: C 682 ILE cc_start: 0.8286 (tp) cc_final: 0.7858 (tp) REVERT: C 711 LYS cc_start: 0.9262 (mmtt) cc_final: 0.8753 (mmtm) REVERT: C 712 GLU cc_start: 0.8697 (tt0) cc_final: 0.7930 (tt0) REVERT: C 716 LEU cc_start: 0.8651 (mt) cc_final: 0.8421 (mt) REVERT: C 719 ASP cc_start: 0.7981 (m-30) cc_final: 0.7754 (m-30) REVERT: C 720 TYR cc_start: 0.7507 (t80) cc_final: 0.6851 (t80) REVERT: C 735 ARG cc_start: 0.7863 (ttm-80) cc_final: 0.7414 (ttm-80) REVERT: C 738 HIS cc_start: 0.7555 (t-90) cc_final: 0.7345 (t-170) REVERT: C 743 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7735 (mm-30) REVERT: C 748 TYR cc_start: 0.6812 (t80) cc_final: 0.6542 (t80) REVERT: C 855 LYS cc_start: 0.8802 (tttt) cc_final: 0.8034 (tppt) outliers start: 0 outliers final: 0 residues processed: 522 average time/residue: 0.3089 time to fit residues: 216.6769 Evaluate side-chains 485 residues out of total 1514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 485 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 133 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN B 97 GLN B 100 ASN ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 GLN ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 ASN A 455 ASN ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 ASN ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 ASN C 455 ASN C 625 ASN ** C 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.5328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 13522 Z= 0.402 Angle : 0.812 10.813 18260 Z= 0.440 Chirality : 0.049 0.299 2014 Planarity : 0.006 0.071 2372 Dihedral : 6.091 25.989 1806 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 27.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.20), residues: 1610 helix: -1.42 (0.16), residues: 812 sheet: -3.01 (0.51), residues: 92 loop : -1.07 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP D 139 HIS 0.008 0.001 HIS B 85 PHE 0.026 0.002 PHE C 633 TYR 0.030 0.002 TYR D 83 ARG 0.010 0.001 ARG A 528 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 1514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 520 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 ASN cc_start: 0.8175 (m-40) cc_final: 0.7877 (m-40) REVERT: B 73 CYS cc_start: 0.7459 (m) cc_final: 0.6749 (p) REVERT: B 75 LYS cc_start: 0.8886 (mtpt) cc_final: 0.8237 (mtmm) REVERT: B 77 TYR cc_start: 0.8233 (m-80) cc_final: 0.7418 (m-80) REVERT: B 79 LYS cc_start: 0.8592 (tppp) cc_final: 0.7137 (tppp) REVERT: B 82 GLU cc_start: 0.8340 (tt0) cc_final: 0.7834 (tt0) REVERT: B 88 TYR cc_start: 0.7337 (p90) cc_final: 0.6994 (p90) REVERT: B 108 ILE cc_start: 0.7963 (mt) cc_final: 0.7657 (tt) REVERT: B 109 ARG cc_start: 0.6071 (mtt-85) cc_final: 0.5859 (mtt-85) REVERT: B 114 GLN cc_start: 0.7628 (mp10) cc_final: 0.7009 (mp10) REVERT: B 128 LYS cc_start: 0.8614 (mttt) cc_final: 0.8403 (mttt) REVERT: B 132 PHE cc_start: 0.7242 (m-80) cc_final: 0.6243 (m-80) REVERT: B 139 TRP cc_start: 0.6354 (m100) cc_final: 0.6090 (m100) REVERT: A 130 GLU cc_start: 0.8575 (pt0) cc_final: 0.7614 (pm20) REVERT: A 138 GLU cc_start: 0.8433 (mp0) cc_final: 0.7954 (mp0) REVERT: A 237 ASP cc_start: 0.8583 (m-30) cc_final: 0.7989 (t0) REVERT: A 270 ASP cc_start: 0.6948 (t70) cc_final: 0.6718 (t0) REVERT: A 287 PHE cc_start: 0.6831 (m-80) cc_final: 0.6370 (m-80) REVERT: A 304 MET cc_start: 0.4744 (tpt) cc_final: 0.4059 (tpt) REVERT: A 315 LYS cc_start: 0.8175 (mmtm) cc_final: 0.7842 (mtmm) REVERT: A 330 LYS cc_start: 0.8266 (mmtm) cc_final: 0.8033 (mmtm) REVERT: A 337 ARG cc_start: 0.8208 (ttm170) cc_final: 0.7396 (ttp80) REVERT: A 338 ARG cc_start: 0.8090 (mtp85) cc_final: 0.7857 (mmm-85) REVERT: A 341 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7588 (mt-10) REVERT: A 344 GLN cc_start: 0.8193 (tp-100) cc_final: 0.7085 (tp-100) REVERT: A 347 ILE cc_start: 0.7955 (mt) cc_final: 0.7729 (mt) REVERT: A 361 LEU cc_start: 0.7583 (tp) cc_final: 0.7207 (tp) REVERT: A 373 LYS cc_start: 0.8213 (mtpp) cc_final: 0.7996 (mtpp) REVERT: A 379 TYR cc_start: 0.7836 (t80) cc_final: 0.7413 (t80) REVERT: A 392 HIS cc_start: 0.8161 (m90) cc_final: 0.7744 (m90) REVERT: A 394 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6366 (mm-30) REVERT: A 407 LEU cc_start: 0.8903 (mt) cc_final: 0.8623 (pp) REVERT: A 411 GLU cc_start: 0.7783 (mt-10) cc_final: 0.6902 (mt-10) REVERT: A 450 ILE cc_start: 0.8124 (mt) cc_final: 0.7896 (mt) REVERT: A 458 LEU cc_start: 0.8686 (tt) cc_final: 0.7913 (tt) REVERT: A 464 TYR cc_start: 0.6848 (t80) cc_final: 0.6408 (t80) REVERT: A 477 PHE cc_start: 0.8002 (m-80) cc_final: 0.7593 (m-80) REVERT: A 478 MET cc_start: 0.8073 (mtp) cc_final: 0.7399 (mtp) REVERT: A 489 LYS cc_start: 0.8210 (mtmm) cc_final: 0.7924 (mtmm) REVERT: A 499 ILE cc_start: 0.8143 (tp) cc_final: 0.7811 (tp) REVERT: A 504 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7368 (mm-30) REVERT: A 505 ARG cc_start: 0.8200 (mtt90) cc_final: 0.7525 (mtt90) REVERT: A 507 ILE cc_start: 0.8510 (mt) cc_final: 0.7923 (mp) REVERT: A 522 TYR cc_start: 0.8016 (m-80) cc_final: 0.7457 (m-80) REVERT: A 534 ASP cc_start: 0.7716 (m-30) cc_final: 0.7494 (m-30) REVERT: A 542 MET cc_start: 0.7885 (tmm) cc_final: 0.7651 (tmm) REVERT: A 545 MET cc_start: 0.7640 (mtm) cc_final: 0.7189 (mtm) REVERT: A 554 GLN cc_start: 0.7059 (tp-100) cc_final: 0.6491 (tp40) REVERT: A 576 GLN cc_start: 0.8064 (tp40) cc_final: 0.7518 (tp40) REVERT: A 593 ASP cc_start: 0.7533 (t0) cc_final: 0.7237 (t0) REVERT: A 617 ILE cc_start: 0.8427 (mm) cc_final: 0.8104 (mm) REVERT: A 635 MET cc_start: 0.7685 (mpp) cc_final: 0.7224 (mpp) REVERT: A 642 MET cc_start: 0.8101 (mmp) cc_final: 0.7690 (mmp) REVERT: A 651 LEU cc_start: 0.8568 (mt) cc_final: 0.8212 (mt) REVERT: A 658 LEU cc_start: 0.8357 (tp) cc_final: 0.8026 (tp) REVERT: A 660 GLN cc_start: 0.8041 (pp30) cc_final: 0.7666 (pp30) REVERT: A 663 LYS cc_start: 0.8111 (ptmm) cc_final: 0.7718 (ttpp) REVERT: A 667 GLU cc_start: 0.8258 (pp20) cc_final: 0.7978 (pp20) REVERT: A 682 ILE cc_start: 0.8638 (tp) cc_final: 0.8181 (tp) REVERT: A 711 LYS cc_start: 0.9251 (mmtt) cc_final: 0.8814 (mmtm) REVERT: A 717 TYR cc_start: 0.8575 (t80) cc_final: 0.8267 (t80) REVERT: A 720 TYR cc_start: 0.7416 (t80) cc_final: 0.6834 (t80) REVERT: A 727 GLU cc_start: 0.7701 (pm20) cc_final: 0.7474 (pm20) REVERT: A 728 LYS cc_start: 0.8558 (ttpt) cc_final: 0.7486 (ptmm) REVERT: A 729 GLN cc_start: 0.7778 (mp10) cc_final: 0.6387 (mp10) REVERT: A 730 PHE cc_start: 0.7519 (t80) cc_final: 0.7317 (t80) REVERT: A 734 ARG cc_start: 0.8494 (ttt-90) cc_final: 0.7659 (ttm-80) REVERT: A 739 MET cc_start: 0.7399 (ptm) cc_final: 0.7199 (ptm) REVERT: A 743 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7776 (mm-30) REVERT: A 750 PHE cc_start: 0.7720 (m-80) cc_final: 0.7480 (m-80) REVERT: A 756 GLU cc_start: 0.7691 (tp30) cc_final: 0.7195 (tp30) REVERT: A 788 ARG cc_start: 0.8288 (ttp80) cc_final: 0.7711 (ttp80) REVERT: A 792 GLU cc_start: 0.8410 (mm-30) cc_final: 0.7962 (mm-30) REVERT: A 805 PHE cc_start: 0.8475 (t80) cc_final: 0.8240 (t80) REVERT: A 806 LEU cc_start: 0.8385 (mt) cc_final: 0.7977 (mt) REVERT: A 822 LYS cc_start: 0.8426 (mptt) cc_final: 0.8125 (mmtm) REVERT: A 862 LEU cc_start: 0.8454 (tt) cc_final: 0.8113 (mt) REVERT: D 65 ASN cc_start: 0.8048 (m-40) cc_final: 0.7786 (m-40) REVERT: D 77 TYR cc_start: 0.8075 (m-80) cc_final: 0.7434 (m-80) REVERT: D 88 TYR cc_start: 0.7161 (p90) cc_final: 0.6898 (p90) REVERT: D 132 PHE cc_start: 0.7235 (m-80) cc_final: 0.6155 (m-80) REVERT: D 136 ARG cc_start: 0.7691 (mmm160) cc_final: 0.6762 (mmm160) REVERT: D 138 ARG cc_start: 0.7336 (ptt-90) cc_final: 0.6329 (ptt-90) REVERT: C 130 GLU cc_start: 0.8528 (pt0) cc_final: 0.7668 (pm20) REVERT: C 237 ASP cc_start: 0.8351 (m-30) cc_final: 0.8003 (t0) REVERT: C 288 ILE cc_start: 0.8537 (tt) cc_final: 0.8326 (tt) REVERT: C 291 MET cc_start: 0.8576 (ttt) cc_final: 0.7858 (ttt) REVERT: C 304 MET cc_start: 0.5353 (tpt) cc_final: 0.5019 (tpt) REVERT: C 315 LYS cc_start: 0.8187 (mtmm) cc_final: 0.7491 (mttt) REVERT: C 337 ARG cc_start: 0.8151 (ttm170) cc_final: 0.7630 (ttp80) REVERT: C 339 MET cc_start: 0.7205 (mtm) cc_final: 0.6930 (mtm) REVERT: C 347 ILE cc_start: 0.7940 (mt) cc_final: 0.7700 (mt) REVERT: C 349 TYR cc_start: 0.7789 (t80) cc_final: 0.7436 (t80) REVERT: C 376 LYS cc_start: 0.8801 (ttpt) cc_final: 0.8318 (tppt) REVERT: C 406 GLU cc_start: 0.7531 (tm-30) cc_final: 0.6926 (tp30) REVERT: C 407 LEU cc_start: 0.8912 (mt) cc_final: 0.8708 (pp) REVERT: C 409 LEU cc_start: 0.8502 (tp) cc_final: 0.8034 (pp) REVERT: C 410 GLN cc_start: 0.8285 (mm-40) cc_final: 0.6591 (mm-40) REVERT: C 447 GLU cc_start: 0.7778 (mp0) cc_final: 0.7444 (tp30) REVERT: C 450 ILE cc_start: 0.8068 (mt) cc_final: 0.7194 (mt) REVERT: C 477 PHE cc_start: 0.7614 (m-80) cc_final: 0.7207 (m-80) REVERT: C 478 MET cc_start: 0.7903 (mtp) cc_final: 0.7629 (mtp) REVERT: C 482 PHE cc_start: 0.8140 (p90) cc_final: 0.7858 (p90) REVERT: C 493 LEU cc_start: 0.7529 (tp) cc_final: 0.7022 (tp) REVERT: C 497 ASN cc_start: 0.7950 (m110) cc_final: 0.7580 (m-40) REVERT: C 501 MET cc_start: 0.7513 (mmp) cc_final: 0.7050 (mmp) REVERT: C 504 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7275 (mm-30) REVERT: C 505 ARG cc_start: 0.8186 (mtt90) cc_final: 0.7749 (mtt90) REVERT: C 507 ILE cc_start: 0.8492 (mt) cc_final: 0.7912 (mp) REVERT: C 522 TYR cc_start: 0.7799 (m-80) cc_final: 0.7087 (m-80) REVERT: C 532 ILE cc_start: 0.8150 (pt) cc_final: 0.7681 (mm) REVERT: C 540 LEU cc_start: 0.8692 (mm) cc_final: 0.8415 (mm) REVERT: C 541 GLU cc_start: 0.8449 (tt0) cc_final: 0.6829 (tm-30) REVERT: C 542 MET cc_start: 0.7773 (tpp) cc_final: 0.7168 (tpp) REVERT: C 543 ILE cc_start: 0.8811 (mt) cc_final: 0.8468 (mt) REVERT: C 555 LEU cc_start: 0.8436 (tp) cc_final: 0.7958 (tp) REVERT: C 576 GLN cc_start: 0.7410 (tm-30) cc_final: 0.6884 (tm-30) REVERT: C 577 LEU cc_start: 0.8728 (mt) cc_final: 0.8353 (mt) REVERT: C 581 GLU cc_start: 0.7947 (pp20) cc_final: 0.7462 (pp20) REVERT: C 589 MET cc_start: 0.5964 (mmt) cc_final: 0.3823 (mmt) REVERT: C 619 LEU cc_start: 0.8751 (tp) cc_final: 0.8549 (tp) REVERT: C 621 LEU cc_start: 0.8081 (mm) cc_final: 0.7653 (mm) REVERT: C 625 ASN cc_start: 0.8224 (m-40) cc_final: 0.7869 (m110) REVERT: C 626 ASN cc_start: 0.8123 (m110) cc_final: 0.7606 (m110) REVERT: C 635 MET cc_start: 0.7824 (mpp) cc_final: 0.7343 (mpp) REVERT: C 641 LEU cc_start: 0.8265 (mt) cc_final: 0.7878 (mm) REVERT: C 642 MET cc_start: 0.7974 (mmp) cc_final: 0.7703 (mmp) REVERT: C 648 PHE cc_start: 0.8815 (p90) cc_final: 0.8612 (p90) REVERT: C 651 LEU cc_start: 0.8631 (mt) cc_final: 0.8162 (mt) REVERT: C 659 TYR cc_start: 0.8931 (t80) cc_final: 0.8725 (t80) REVERT: C 660 GLN cc_start: 0.8530 (mm-40) cc_final: 0.8156 (mm-40) REVERT: C 667 GLU cc_start: 0.7932 (pp20) cc_final: 0.7584 (pp20) REVERT: C 711 LYS cc_start: 0.9274 (mmtt) cc_final: 0.8775 (mmtm) REVERT: C 712 GLU cc_start: 0.8850 (tt0) cc_final: 0.8181 (tt0) REVERT: C 716 LEU cc_start: 0.8847 (mt) cc_final: 0.8612 (mt) REVERT: C 717 TYR cc_start: 0.8604 (t80) cc_final: 0.8354 (t80) REVERT: C 720 TYR cc_start: 0.7612 (t80) cc_final: 0.7052 (t80) REVERT: C 729 GLN cc_start: 0.8191 (mp10) cc_final: 0.7980 (mp10) REVERT: C 730 PHE cc_start: 0.7543 (t80) cc_final: 0.7319 (t80) REVERT: C 735 ARG cc_start: 0.7977 (ttm-80) cc_final: 0.7681 (ttm-80) REVERT: C 739 MET cc_start: 0.7483 (ptm) cc_final: 0.7245 (ptm) REVERT: C 743 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7948 (mm-30) REVERT: C 748 TYR cc_start: 0.6965 (t80) cc_final: 0.6608 (t80) REVERT: C 750 PHE cc_start: 0.7856 (m-10) cc_final: 0.7580 (m-10) REVERT: C 754 GLU cc_start: 0.8372 (mt-10) cc_final: 0.7795 (mp0) REVERT: C 756 GLU cc_start: 0.7397 (tp30) cc_final: 0.6624 (tp30) REVERT: C 788 ARG cc_start: 0.8424 (ptp-110) cc_final: 0.8051 (ptp-110) REVERT: C 805 PHE cc_start: 0.8477 (t80) cc_final: 0.8151 (t80) REVERT: C 806 LEU cc_start: 0.8322 (mt) cc_final: 0.7747 (mt) REVERT: C 855 LYS cc_start: 0.8666 (tttt) cc_final: 0.7909 (tptp) outliers start: 0 outliers final: 0 residues processed: 520 average time/residue: 0.3222 time to fit residues: 223.5637 Evaluate side-chains 485 residues out of total 1514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 485 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 156 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 HIS A 768 GLN ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.5729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13522 Z= 0.265 Angle : 0.703 11.912 18260 Z= 0.365 Chirality : 0.046 0.200 2014 Planarity : 0.005 0.039 2372 Dihedral : 5.605 24.100 1806 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 22.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.20), residues: 1610 helix: -1.18 (0.17), residues: 802 sheet: -3.01 (0.57), residues: 72 loop : -1.17 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP A 328 HIS 0.005 0.001 HIS A 531 PHE 0.022 0.002 PHE A 790 TYR 0.018 0.002 TYR C 301 ARG 0.008 0.001 ARG A 763 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 504 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 18 LYS cc_start: 0.8025 (mmtm) cc_final: 0.7363 (mmmm) REVERT: B 22 LEU cc_start: 0.8361 (mm) cc_final: 0.8114 (mm) REVERT: B 65 ASN cc_start: 0.7826 (m-40) cc_final: 0.7428 (m-40) REVERT: B 75 LYS cc_start: 0.8869 (mtpt) cc_final: 0.8202 (mtmm) REVERT: B 77 TYR cc_start: 0.8227 (m-80) cc_final: 0.7726 (m-80) REVERT: B 79 LYS cc_start: 0.8481 (tppp) cc_final: 0.7016 (tppp) REVERT: B 82 GLU cc_start: 0.8378 (tt0) cc_final: 0.7692 (tt0) REVERT: B 88 TYR cc_start: 0.7184 (p90) cc_final: 0.6884 (p90) REVERT: B 108 ILE cc_start: 0.7965 (mt) cc_final: 0.7196 (tt) REVERT: B 114 GLN cc_start: 0.7515 (mp10) cc_final: 0.7192 (mp10) REVERT: B 124 ARG cc_start: 0.8494 (ttt-90) cc_final: 0.8275 (ttt-90) REVERT: B 128 LYS cc_start: 0.8508 (mttt) cc_final: 0.8297 (mttt) REVERT: A 130 GLU cc_start: 0.8527 (pt0) cc_final: 0.7508 (pm20) REVERT: A 237 ASP cc_start: 0.8525 (m-30) cc_final: 0.7945 (t0) REVERT: A 270 ASP cc_start: 0.6992 (t70) cc_final: 0.6687 (t0) REVERT: A 287 PHE cc_start: 0.6788 (m-80) cc_final: 0.5810 (m-80) REVERT: A 291 MET cc_start: 0.8267 (ttt) cc_final: 0.7886 (ttp) REVERT: A 304 MET cc_start: 0.4673 (tpt) cc_final: 0.4100 (tpt) REVERT: A 313 MET cc_start: 0.7309 (ttm) cc_final: 0.6813 (ttm) REVERT: A 315 LYS cc_start: 0.8107 (mmtm) cc_final: 0.7786 (mttt) REVERT: A 330 LYS cc_start: 0.8296 (mmtm) cc_final: 0.8089 (mmtm) REVERT: A 332 ASN cc_start: 0.7774 (t0) cc_final: 0.7204 (t0) REVERT: A 337 ARG cc_start: 0.8227 (ttm170) cc_final: 0.7452 (ttp80) REVERT: A 341 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7923 (mt-10) REVERT: A 343 PHE cc_start: 0.8715 (m-80) cc_final: 0.8474 (m-80) REVERT: A 347 ILE cc_start: 0.7854 (mt) cc_final: 0.7632 (mt) REVERT: A 361 LEU cc_start: 0.7501 (tp) cc_final: 0.7241 (tp) REVERT: A 392 HIS cc_start: 0.8222 (m90) cc_final: 0.7805 (m90) REVERT: A 407 LEU cc_start: 0.8870 (mt) cc_final: 0.8373 (pp) REVERT: A 411 GLU cc_start: 0.7702 (mt-10) cc_final: 0.6820 (mt-10) REVERT: A 446 PHE cc_start: 0.7485 (m-80) cc_final: 0.7096 (m-80) REVERT: A 447 GLU cc_start: 0.7585 (pm20) cc_final: 0.7279 (tp30) REVERT: A 450 ILE cc_start: 0.8160 (mt) cc_final: 0.6944 (mt) REVERT: A 459 GLU cc_start: 0.6991 (mm-30) cc_final: 0.6437 (mm-30) REVERT: A 463 ASP cc_start: 0.7761 (m-30) cc_final: 0.7037 (t70) REVERT: A 464 TYR cc_start: 0.6784 (t80) cc_final: 0.6308 (t80) REVERT: A 477 PHE cc_start: 0.7673 (m-80) cc_final: 0.7419 (m-80) REVERT: A 478 MET cc_start: 0.8107 (mtp) cc_final: 0.6944 (mtp) REVERT: A 497 ASN cc_start: 0.7845 (m-40) cc_final: 0.7569 (m-40) REVERT: A 499 ILE cc_start: 0.7986 (tp) cc_final: 0.7651 (tp) REVERT: A 504 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7105 (mm-30) REVERT: A 505 ARG cc_start: 0.8155 (mtt90) cc_final: 0.7555 (mtt90) REVERT: A 506 ARG cc_start: 0.8007 (mtt90) cc_final: 0.7407 (mtt-85) REVERT: A 507 ILE cc_start: 0.8515 (mt) cc_final: 0.7878 (mt) REVERT: A 522 TYR cc_start: 0.7706 (m-80) cc_final: 0.6949 (m-80) REVERT: A 533 ILE cc_start: 0.8452 (pt) cc_final: 0.7583 (mp) REVERT: A 534 ASP cc_start: 0.7646 (m-30) cc_final: 0.7429 (m-30) REVERT: A 543 ILE cc_start: 0.8661 (mt) cc_final: 0.7846 (mt) REVERT: A 545 MET cc_start: 0.7578 (mtm) cc_final: 0.7107 (mtm) REVERT: A 550 ASP cc_start: 0.7436 (p0) cc_final: 0.7168 (p0) REVERT: A 554 GLN cc_start: 0.7095 (tp-100) cc_final: 0.6664 (tp40) REVERT: A 576 GLN cc_start: 0.7878 (tp40) cc_final: 0.7256 (tp40) REVERT: A 593 ASP cc_start: 0.7438 (t0) cc_final: 0.7163 (t0) REVERT: A 626 ASN cc_start: 0.8053 (m110) cc_final: 0.7745 (m110) REVERT: A 635 MET cc_start: 0.7668 (mpp) cc_final: 0.7193 (mpp) REVERT: A 642 MET cc_start: 0.8168 (mmp) cc_final: 0.7796 (mmp) REVERT: A 651 LEU cc_start: 0.8410 (mt) cc_final: 0.8031 (mt) REVERT: A 658 LEU cc_start: 0.8252 (tp) cc_final: 0.7997 (tp) REVERT: A 660 GLN cc_start: 0.7969 (pp30) cc_final: 0.7340 (pp30) REVERT: A 663 LYS cc_start: 0.8104 (ptmm) cc_final: 0.7531 (ttpp) REVERT: A 667 GLU cc_start: 0.8224 (pp20) cc_final: 0.7912 (pp20) REVERT: A 676 MET cc_start: 0.6643 (tmm) cc_final: 0.6443 (tmm) REVERT: A 682 ILE cc_start: 0.8696 (tp) cc_final: 0.8433 (tp) REVERT: A 711 LYS cc_start: 0.9236 (mmtt) cc_final: 0.8760 (mmtm) REVERT: A 716 LEU cc_start: 0.8782 (mt) cc_final: 0.8290 (pp) REVERT: A 717 TYR cc_start: 0.8555 (t80) cc_final: 0.7982 (t80) REVERT: A 720 TYR cc_start: 0.7385 (t80) cc_final: 0.6968 (t80) REVERT: A 728 LYS cc_start: 0.8459 (ttpt) cc_final: 0.7628 (ptmm) REVERT: A 743 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7591 (mm-30) REVERT: A 750 PHE cc_start: 0.7693 (m-80) cc_final: 0.7356 (m-10) REVERT: A 756 GLU cc_start: 0.7618 (tp30) cc_final: 0.7188 (tp30) REVERT: A 788 ARG cc_start: 0.8265 (ttp80) cc_final: 0.7347 (ttp80) REVERT: A 792 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7485 (mm-30) REVERT: A 805 PHE cc_start: 0.8353 (t80) cc_final: 0.8069 (t80) REVERT: A 806 LEU cc_start: 0.8245 (mt) cc_final: 0.7793 (mt) REVERT: A 822 LYS cc_start: 0.8321 (mptt) cc_final: 0.8102 (mmtm) REVERT: A 855 LYS cc_start: 0.8672 (tttt) cc_final: 0.8119 (ttpp) REVERT: D 22 LEU cc_start: 0.8311 (mm) cc_final: 0.8088 (mm) REVERT: D 65 ASN cc_start: 0.7788 (m-40) cc_final: 0.7374 (m-40) REVERT: D 77 TYR cc_start: 0.7947 (m-80) cc_final: 0.7528 (m-80) REVERT: D 82 GLU cc_start: 0.8244 (tt0) cc_final: 0.8021 (tt0) REVERT: D 88 TYR cc_start: 0.6931 (p90) cc_final: 0.6681 (p90) REVERT: D 108 ILE cc_start: 0.7965 (mt) cc_final: 0.7742 (mt) REVERT: D 136 ARG cc_start: 0.7653 (mmm160) cc_final: 0.6768 (mmm160) REVERT: D 138 ARG cc_start: 0.7154 (ptt-90) cc_final: 0.6011 (ptt-90) REVERT: C 130 GLU cc_start: 0.8521 (pt0) cc_final: 0.7604 (pm20) REVERT: C 138 GLU cc_start: 0.8413 (mp0) cc_final: 0.7813 (mp0) REVERT: C 237 ASP cc_start: 0.8315 (m-30) cc_final: 0.7927 (t0) REVERT: C 304 MET cc_start: 0.5044 (tpt) cc_final: 0.4721 (tpt) REVERT: C 315 LYS cc_start: 0.8121 (mtmm) cc_final: 0.7425 (mttt) REVERT: C 347 ILE cc_start: 0.7819 (mt) cc_final: 0.7587 (mt) REVERT: C 349 TYR cc_start: 0.7719 (t80) cc_final: 0.7382 (t80) REVERT: C 376 LYS cc_start: 0.8699 (ttpt) cc_final: 0.8212 (tppt) REVERT: C 392 HIS cc_start: 0.7960 (m-70) cc_final: 0.7432 (m-70) REVERT: C 407 LEU cc_start: 0.8969 (mt) cc_final: 0.8741 (pp) REVERT: C 410 GLN cc_start: 0.8179 (mm-40) cc_final: 0.7142 (mm-40) REVERT: C 447 GLU cc_start: 0.7755 (mp0) cc_final: 0.7463 (tp30) REVERT: C 450 ILE cc_start: 0.8164 (mt) cc_final: 0.7397 (mt) REVERT: C 477 PHE cc_start: 0.7497 (m-80) cc_final: 0.7149 (m-80) REVERT: C 478 MET cc_start: 0.7889 (mtp) cc_final: 0.7529 (mtp) REVERT: C 482 PHE cc_start: 0.8097 (p90) cc_final: 0.7827 (p90) REVERT: C 497 ASN cc_start: 0.7679 (m110) cc_final: 0.7322 (m-40) REVERT: C 499 ILE cc_start: 0.7919 (tp) cc_final: 0.7627 (tp) REVERT: C 501 MET cc_start: 0.7275 (mmp) cc_final: 0.6785 (mmp) REVERT: C 504 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7193 (mm-30) REVERT: C 505 ARG cc_start: 0.8135 (mtt90) cc_final: 0.7679 (mtt90) REVERT: C 507 ILE cc_start: 0.8438 (mt) cc_final: 0.7956 (mt) REVERT: C 522 TYR cc_start: 0.7639 (m-80) cc_final: 0.6883 (m-80) REVERT: C 530 ASP cc_start: 0.7913 (p0) cc_final: 0.7627 (p0) REVERT: C 540 LEU cc_start: 0.8669 (mm) cc_final: 0.8407 (mm) REVERT: C 541 GLU cc_start: 0.8295 (tt0) cc_final: 0.7363 (tt0) REVERT: C 542 MET cc_start: 0.7684 (tpp) cc_final: 0.7184 (tpp) REVERT: C 543 ILE cc_start: 0.8781 (mt) cc_final: 0.8457 (mt) REVERT: C 545 MET cc_start: 0.7595 (mtm) cc_final: 0.7158 (mtm) REVERT: C 555 LEU cc_start: 0.8285 (tp) cc_final: 0.7867 (tp) REVERT: C 576 GLN cc_start: 0.7174 (tm-30) cc_final: 0.6691 (tm-30) REVERT: C 577 LEU cc_start: 0.8618 (mt) cc_final: 0.8274 (mt) REVERT: C 581 GLU cc_start: 0.7891 (pp20) cc_final: 0.7490 (pp20) REVERT: C 617 ILE cc_start: 0.8493 (mm) cc_final: 0.8285 (mm) REVERT: C 621 LEU cc_start: 0.7998 (mm) cc_final: 0.7469 (mm) REVERT: C 625 ASN cc_start: 0.8089 (m-40) cc_final: 0.7669 (m110) REVERT: C 626 ASN cc_start: 0.8023 (m110) cc_final: 0.7503 (m110) REVERT: C 635 MET cc_start: 0.7805 (mpp) cc_final: 0.7313 (mpp) REVERT: C 641 LEU cc_start: 0.8261 (mt) cc_final: 0.7937 (mm) REVERT: C 642 MET cc_start: 0.7871 (mmp) cc_final: 0.7573 (mmp) REVERT: C 648 PHE cc_start: 0.8709 (p90) cc_final: 0.8469 (p90) REVERT: C 651 LEU cc_start: 0.8522 (mt) cc_final: 0.8013 (mt) REVERT: C 659 TYR cc_start: 0.8784 (t80) cc_final: 0.8459 (t80) REVERT: C 660 GLN cc_start: 0.8534 (mm-40) cc_final: 0.8126 (mm-40) REVERT: C 667 GLU cc_start: 0.7905 (pp20) cc_final: 0.7530 (pp20) REVERT: C 682 ILE cc_start: 0.8261 (tp) cc_final: 0.7859 (tp) REVERT: C 711 LYS cc_start: 0.9275 (mmtt) cc_final: 0.8753 (mmtm) REVERT: C 712 GLU cc_start: 0.8791 (tt0) cc_final: 0.8036 (tt0) REVERT: C 716 LEU cc_start: 0.8846 (mt) cc_final: 0.8539 (mp) REVERT: C 717 TYR cc_start: 0.8630 (t80) cc_final: 0.8289 (t80) REVERT: C 719 ASP cc_start: 0.7926 (m-30) cc_final: 0.7447 (m-30) REVERT: C 720 TYR cc_start: 0.7548 (t80) cc_final: 0.7094 (t80) REVERT: C 730 PHE cc_start: 0.7438 (t80) cc_final: 0.7205 (t80) REVERT: C 735 ARG cc_start: 0.7833 (ttm-80) cc_final: 0.7521 (ttm-80) REVERT: C 738 HIS cc_start: 0.7868 (t70) cc_final: 0.7269 (t-170) REVERT: C 743 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7672 (mm-30) REVERT: C 747 LYS cc_start: 0.9041 (mtpt) cc_final: 0.8774 (mmmt) REVERT: C 748 TYR cc_start: 0.6928 (t80) cc_final: 0.6603 (t80) REVERT: C 756 GLU cc_start: 0.7222 (tp30) cc_final: 0.6560 (tp30) REVERT: C 788 ARG cc_start: 0.8448 (ptp-110) cc_final: 0.8043 (ptp-110) REVERT: C 801 GLN cc_start: 0.8402 (mp10) cc_final: 0.8073 (mp10) REVERT: C 805 PHE cc_start: 0.8400 (t80) cc_final: 0.8045 (t80) REVERT: C 806 LEU cc_start: 0.8330 (mt) cc_final: 0.7736 (mt) REVERT: C 822 LYS cc_start: 0.8492 (mmtt) cc_final: 0.8261 (mmtm) REVERT: C 855 LYS cc_start: 0.8544 (tttt) cc_final: 0.7910 (tptp) outliers start: 0 outliers final: 0 residues processed: 504 average time/residue: 0.3116 time to fit residues: 213.6723 Evaluate side-chains 490 residues out of total 1514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 490 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 88 optimal weight: 0.5980 chunk 131 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 156 optimal weight: 0.0980 chunk 97 optimal weight: 5.9990 chunk 95 optimal weight: 0.2980 chunk 72 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 ASN ** C 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.6017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13522 Z= 0.171 Angle : 0.644 10.790 18260 Z= 0.324 Chirality : 0.044 0.195 2014 Planarity : 0.004 0.041 2372 Dihedral : 5.183 23.142 1806 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.20), residues: 1610 helix: -0.70 (0.18), residues: 806 sheet: -3.04 (0.57), residues: 68 loop : -0.93 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP B 139 HIS 0.006 0.001 HIS A 738 PHE 0.017 0.001 PHE C 446 TYR 0.021 0.001 TYR A 659 ARG 0.007 0.000 ARG A 763 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 1514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 513 time to evaluate : 2.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 LEU cc_start: 0.8345 (mm) cc_final: 0.8081 (mm) REVERT: B 77 TYR cc_start: 0.7972 (m-80) cc_final: 0.7577 (m-80) REVERT: B 79 LYS cc_start: 0.8232 (tppp) cc_final: 0.6807 (tppp) REVERT: B 82 GLU cc_start: 0.8175 (tt0) cc_final: 0.7499 (tt0) REVERT: B 98 GLN cc_start: 0.8854 (mp10) cc_final: 0.8531 (mp10) REVERT: B 108 ILE cc_start: 0.8085 (mt) cc_final: 0.7640 (tt) REVERT: B 124 ARG cc_start: 0.8491 (ttt-90) cc_final: 0.8009 (ttt-90) REVERT: B 128 LYS cc_start: 0.8554 (mttt) cc_final: 0.8348 (mttt) REVERT: B 132 PHE cc_start: 0.6717 (m-10) cc_final: 0.6221 (m-10) REVERT: A 130 GLU cc_start: 0.8485 (pt0) cc_final: 0.7439 (pm20) REVERT: A 237 ASP cc_start: 0.8410 (m-30) cc_final: 0.7815 (t0) REVERT: A 270 ASP cc_start: 0.6885 (t70) cc_final: 0.6599 (t0) REVERT: A 288 ILE cc_start: 0.8656 (mp) cc_final: 0.8071 (mp) REVERT: A 291 MET cc_start: 0.8257 (ttt) cc_final: 0.7840 (ptm) REVERT: A 292 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7779 (mm-30) REVERT: A 304 MET cc_start: 0.4577 (tpt) cc_final: 0.3959 (tpt) REVERT: A 315 LYS cc_start: 0.8061 (mmtm) cc_final: 0.7677 (mttt) REVERT: A 328 TRP cc_start: 0.6577 (m100) cc_final: 0.6332 (m100) REVERT: A 332 ASN cc_start: 0.7686 (t0) cc_final: 0.7137 (t0) REVERT: A 337 ARG cc_start: 0.8148 (ttm170) cc_final: 0.7262 (ttp80) REVERT: A 341 GLU cc_start: 0.8400 (mt-10) cc_final: 0.7873 (mt-10) REVERT: A 347 ILE cc_start: 0.7699 (mt) cc_final: 0.6863 (tp) REVERT: A 349 TYR cc_start: 0.7507 (t80) cc_final: 0.7281 (t80) REVERT: A 361 LEU cc_start: 0.7193 (tp) cc_final: 0.6834 (tp) REVERT: A 392 HIS cc_start: 0.8170 (m90) cc_final: 0.7745 (m90) REVERT: A 407 LEU cc_start: 0.8901 (mt) cc_final: 0.8462 (pp) REVERT: A 408 THR cc_start: 0.8088 (m) cc_final: 0.7468 (p) REVERT: A 410 GLN cc_start: 0.8222 (mp-120) cc_final: 0.7707 (mm-40) REVERT: A 411 GLU cc_start: 0.7639 (mt-10) cc_final: 0.6779 (mt-10) REVERT: A 432 LEU cc_start: 0.8228 (mt) cc_final: 0.7978 (mt) REVERT: A 446 PHE cc_start: 0.7732 (m-80) cc_final: 0.7162 (m-80) REVERT: A 449 PHE cc_start: 0.7211 (m-10) cc_final: 0.6977 (m-10) REVERT: A 458 LEU cc_start: 0.8525 (tp) cc_final: 0.8313 (tp) REVERT: A 463 ASP cc_start: 0.7781 (m-30) cc_final: 0.7512 (m-30) REVERT: A 478 MET cc_start: 0.7987 (mtp) cc_final: 0.7251 (mtp) REVERT: A 499 ILE cc_start: 0.7791 (tp) cc_final: 0.7514 (tp) REVERT: A 501 MET cc_start: 0.7549 (mtt) cc_final: 0.6676 (mmt) REVERT: A 504 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7119 (mm-30) REVERT: A 505 ARG cc_start: 0.8107 (mtt90) cc_final: 0.7403 (mtt90) REVERT: A 506 ARG cc_start: 0.7914 (mtt90) cc_final: 0.7655 (mtt90) REVERT: A 507 ILE cc_start: 0.8474 (mt) cc_final: 0.7864 (mt) REVERT: A 522 TYR cc_start: 0.7584 (m-80) cc_final: 0.6689 (m-80) REVERT: A 533 ILE cc_start: 0.8562 (pt) cc_final: 0.8143 (mp) REVERT: A 539 ARG cc_start: 0.8050 (ttm-80) cc_final: 0.7828 (ptp-110) REVERT: A 540 LEU cc_start: 0.8777 (mm) cc_final: 0.8524 (mm) REVERT: A 542 MET cc_start: 0.7677 (tmm) cc_final: 0.7438 (tmm) REVERT: A 543 ILE cc_start: 0.8524 (mt) cc_final: 0.7902 (mt) REVERT: A 545 MET cc_start: 0.7494 (mtm) cc_final: 0.7121 (mtm) REVERT: A 553 LYS cc_start: 0.8275 (tppp) cc_final: 0.7709 (ttmm) REVERT: A 572 LYS cc_start: 0.8141 (tptt) cc_final: 0.7521 (tptp) REVERT: A 573 GLU cc_start: 0.7582 (pm20) cc_final: 0.7332 (pm20) REVERT: A 593 ASP cc_start: 0.7486 (t0) cc_final: 0.7208 (t0) REVERT: A 617 ILE cc_start: 0.8342 (mm) cc_final: 0.8131 (mm) REVERT: A 619 LEU cc_start: 0.8658 (tp) cc_final: 0.8407 (tp) REVERT: A 626 ASN cc_start: 0.7901 (m110) cc_final: 0.7557 (m110) REVERT: A 635 MET cc_start: 0.7616 (mpp) cc_final: 0.7084 (mpp) REVERT: A 642 MET cc_start: 0.8066 (mmp) cc_final: 0.7700 (mmp) REVERT: A 648 PHE cc_start: 0.8619 (p90) cc_final: 0.8336 (p90) REVERT: A 651 LEU cc_start: 0.8357 (mt) cc_final: 0.7908 (mt) REVERT: A 658 LEU cc_start: 0.8068 (tp) cc_final: 0.7788 (tp) REVERT: A 659 TYR cc_start: 0.8569 (t80) cc_final: 0.8134 (t80) REVERT: A 660 GLN cc_start: 0.8017 (pp30) cc_final: 0.7385 (pp30) REVERT: A 663 LYS cc_start: 0.8047 (ptmm) cc_final: 0.7320 (mptt) REVERT: A 667 GLU cc_start: 0.8255 (pp20) cc_final: 0.7945 (pp20) REVERT: A 711 LYS cc_start: 0.9240 (mmtt) cc_final: 0.8760 (mmtm) REVERT: A 712 GLU cc_start: 0.8779 (tt0) cc_final: 0.8371 (tt0) REVERT: A 716 LEU cc_start: 0.8784 (mt) cc_final: 0.8273 (pp) REVERT: A 717 TYR cc_start: 0.8574 (t80) cc_final: 0.8083 (t80) REVERT: A 720 TYR cc_start: 0.7366 (t80) cc_final: 0.6949 (t80) REVERT: A 727 GLU cc_start: 0.7513 (pm20) cc_final: 0.7272 (pm20) REVERT: A 734 ARG cc_start: 0.8449 (ttt-90) cc_final: 0.7920 (ttt180) REVERT: A 735 ARG cc_start: 0.7866 (ttm170) cc_final: 0.7490 (ttm170) REVERT: A 739 MET cc_start: 0.7235 (ptm) cc_final: 0.6987 (ptm) REVERT: A 743 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7456 (mm-30) REVERT: A 750 PHE cc_start: 0.7567 (m-80) cc_final: 0.7175 (m-80) REVERT: A 754 GLU cc_start: 0.8407 (mt-10) cc_final: 0.7900 (mp0) REVERT: A 756 GLU cc_start: 0.7495 (tp30) cc_final: 0.7104 (tp30) REVERT: A 763 ARG cc_start: 0.6612 (tpp80) cc_final: 0.6114 (ttm110) REVERT: A 788 ARG cc_start: 0.8178 (ttp80) cc_final: 0.7380 (ttp80) REVERT: A 792 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7523 (mm-30) REVERT: A 805 PHE cc_start: 0.8265 (t80) cc_final: 0.7991 (t80) REVERT: A 806 LEU cc_start: 0.8303 (mt) cc_final: 0.7844 (mt) REVERT: A 822 LYS cc_start: 0.8194 (mptt) cc_final: 0.7910 (mmtm) REVERT: A 855 LYS cc_start: 0.8760 (tttt) cc_final: 0.8141 (ttpp) REVERT: D 18 LYS cc_start: 0.7804 (mmtm) cc_final: 0.7201 (mmmm) REVERT: D 22 LEU cc_start: 0.8370 (mm) cc_final: 0.8007 (mm) REVERT: D 65 ASN cc_start: 0.7386 (m-40) cc_final: 0.7042 (m-40) REVERT: D 77 TYR cc_start: 0.7909 (m-80) cc_final: 0.7449 (m-80) REVERT: D 132 PHE cc_start: 0.7074 (m-80) cc_final: 0.6218 (m-80) REVERT: D 138 ARG cc_start: 0.6963 (ptt-90) cc_final: 0.6044 (ptt-90) REVERT: C 130 GLU cc_start: 0.8489 (pt0) cc_final: 0.7552 (pm20) REVERT: C 237 ASP cc_start: 0.8299 (m-30) cc_final: 0.7838 (t70) REVERT: C 287 PHE cc_start: 0.6762 (m-80) cc_final: 0.6484 (m-80) REVERT: C 291 MET cc_start: 0.8334 (ttt) cc_final: 0.8100 (ttt) REVERT: C 304 MET cc_start: 0.4943 (tpt) cc_final: 0.4586 (tpt) REVERT: C 315 LYS cc_start: 0.8107 (mtmm) cc_final: 0.7367 (mttt) REVERT: C 328 TRP cc_start: 0.6524 (m100) cc_final: 0.5971 (m100) REVERT: C 332 ASN cc_start: 0.7703 (t0) cc_final: 0.7324 (t0) REVERT: C 337 ARG cc_start: 0.8050 (ptt90) cc_final: 0.7379 (ttp80) REVERT: C 344 GLN cc_start: 0.8176 (tp-100) cc_final: 0.7194 (tp-100) REVERT: C 347 ILE cc_start: 0.7684 (mt) cc_final: 0.7401 (mt) REVERT: C 349 TYR cc_start: 0.7596 (t80) cc_final: 0.7272 (t80) REVERT: C 376 LYS cc_start: 0.8660 (ttpt) cc_final: 0.8116 (tppt) REVERT: C 382 ASN cc_start: 0.8179 (m110) cc_final: 0.7949 (t0) REVERT: C 392 HIS cc_start: 0.7930 (m-70) cc_final: 0.7416 (m-70) REVERT: C 406 GLU cc_start: 0.7010 (tm-30) cc_final: 0.6790 (tp30) REVERT: C 407 LEU cc_start: 0.8949 (mt) cc_final: 0.8715 (pp) REVERT: C 410 GLN cc_start: 0.8076 (mm-40) cc_final: 0.7188 (mm-40) REVERT: C 447 GLU cc_start: 0.7683 (mp0) cc_final: 0.7432 (tp30) REVERT: C 450 ILE cc_start: 0.8242 (mt) cc_final: 0.7199 (mt) REVERT: C 477 PHE cc_start: 0.7294 (m-80) cc_final: 0.7081 (m-80) REVERT: C 478 MET cc_start: 0.7844 (mtp) cc_final: 0.7422 (mtp) REVERT: C 482 PHE cc_start: 0.7998 (p90) cc_final: 0.7455 (p90) REVERT: C 504 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7087 (mm-30) REVERT: C 505 ARG cc_start: 0.8091 (mtt90) cc_final: 0.7597 (mtt90) REVERT: C 506 ARG cc_start: 0.7875 (mtt90) cc_final: 0.7128 (mtt90) REVERT: C 507 ILE cc_start: 0.8361 (mt) cc_final: 0.7906 (mt) REVERT: C 530 ASP cc_start: 0.7750 (p0) cc_final: 0.7306 (p0) REVERT: C 532 ILE cc_start: 0.8083 (pt) cc_final: 0.7882 (pt) REVERT: C 541 GLU cc_start: 0.8064 (tt0) cc_final: 0.7056 (tt0) REVERT: C 542 MET cc_start: 0.7640 (tpp) cc_final: 0.7112 (tpp) REVERT: C 545 MET cc_start: 0.7476 (mtm) cc_final: 0.7134 (mtm) REVERT: C 553 LYS cc_start: 0.7905 (tppp) cc_final: 0.7528 (ttmm) REVERT: C 554 GLN cc_start: 0.7022 (mm-40) cc_final: 0.6642 (mm110) REVERT: C 555 LEU cc_start: 0.8271 (tp) cc_final: 0.7858 (tp) REVERT: C 576 GLN cc_start: 0.7559 (tm-30) cc_final: 0.7068 (tm-30) REVERT: C 577 LEU cc_start: 0.8645 (mt) cc_final: 0.8246 (pp) REVERT: C 581 GLU cc_start: 0.7748 (pp20) cc_final: 0.7403 (pp20) REVERT: C 617 ILE cc_start: 0.8386 (mm) cc_final: 0.8083 (mm) REVERT: C 619 LEU cc_start: 0.8670 (tp) cc_final: 0.8468 (tp) REVERT: C 621 LEU cc_start: 0.7999 (mm) cc_final: 0.7409 (mm) REVERT: C 625 ASN cc_start: 0.7999 (m-40) cc_final: 0.7545 (m110) REVERT: C 626 ASN cc_start: 0.7944 (m110) cc_final: 0.7417 (m110) REVERT: C 635 MET cc_start: 0.7705 (mpp) cc_final: 0.7209 (mpp) REVERT: C 640 LYS cc_start: 0.7749 (mtpp) cc_final: 0.7480 (mtpp) REVERT: C 641 LEU cc_start: 0.8264 (mt) cc_final: 0.7942 (mm) REVERT: C 642 MET cc_start: 0.7838 (mmp) cc_final: 0.7464 (mmp) REVERT: C 648 PHE cc_start: 0.8596 (p90) cc_final: 0.8180 (p90) REVERT: C 651 LEU cc_start: 0.8552 (mt) cc_final: 0.7952 (mt) REVERT: C 659 TYR cc_start: 0.8716 (t80) cc_final: 0.8184 (t80) REVERT: C 660 GLN cc_start: 0.8458 (mm-40) cc_final: 0.8242 (mm-40) REVERT: C 663 LYS cc_start: 0.7948 (ptmm) cc_final: 0.7434 (mmtt) REVERT: C 666 LEU cc_start: 0.8561 (mm) cc_final: 0.8326 (mm) REVERT: C 667 GLU cc_start: 0.7875 (pp20) cc_final: 0.7549 (pp20) REVERT: C 682 ILE cc_start: 0.8108 (tp) cc_final: 0.7117 (tp) REVERT: C 711 LYS cc_start: 0.9270 (mmtt) cc_final: 0.8751 (mmtm) REVERT: C 712 GLU cc_start: 0.8772 (tt0) cc_final: 0.8041 (tt0) REVERT: C 716 LEU cc_start: 0.8839 (mt) cc_final: 0.8540 (mp) REVERT: C 717 TYR cc_start: 0.8592 (t80) cc_final: 0.8229 (t80) REVERT: C 719 ASP cc_start: 0.7930 (m-30) cc_final: 0.7601 (m-30) REVERT: C 720 TYR cc_start: 0.7501 (t80) cc_final: 0.7057 (t80) REVERT: C 730 PHE cc_start: 0.7377 (t80) cc_final: 0.7057 (t80) REVERT: C 738 HIS cc_start: 0.7696 (t70) cc_final: 0.6999 (t70) REVERT: C 739 MET cc_start: 0.7363 (ptm) cc_final: 0.7161 (ptm) REVERT: C 743 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7306 (mm-30) REVERT: C 747 LYS cc_start: 0.8958 (mtpt) cc_final: 0.8710 (mmmt) REVERT: C 748 TYR cc_start: 0.6795 (t80) cc_final: 0.6541 (t80) REVERT: C 754 GLU cc_start: 0.8283 (mt-10) cc_final: 0.8062 (mt-10) REVERT: C 756 GLU cc_start: 0.7016 (tp30) cc_final: 0.6400 (tp30) REVERT: C 788 ARG cc_start: 0.8354 (ptp-110) cc_final: 0.7865 (ptp-110) REVERT: C 805 PHE cc_start: 0.8293 (t80) cc_final: 0.7945 (t80) REVERT: C 806 LEU cc_start: 0.8182 (mt) cc_final: 0.7605 (mt) REVERT: C 835 GLU cc_start: 0.7499 (pm20) cc_final: 0.7296 (pm20) REVERT: C 855 LYS cc_start: 0.8700 (tttt) cc_final: 0.8302 (mmtt) outliers start: 0 outliers final: 0 residues processed: 513 average time/residue: 0.3134 time to fit residues: 217.6514 Evaluate side-chains 489 residues out of total 1514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 489 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 99 optimal weight: 0.2980 chunk 106 optimal weight: 0.6980 chunk 77 optimal weight: 7.9990 chunk 14 optimal weight: 0.0010 chunk 122 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN A 625 ASN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 382 ASN C 455 ASN ** C 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.6330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13522 Z= 0.172 Angle : 0.653 10.102 18260 Z= 0.330 Chirality : 0.044 0.298 2014 Planarity : 0.005 0.109 2372 Dihedral : 5.119 22.519 1806 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.21), residues: 1610 helix: -0.48 (0.18), residues: 792 sheet: -2.92 (0.59), residues: 68 loop : -0.95 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 139 HIS 0.007 0.001 HIS A 531 PHE 0.032 0.001 PHE C 633 TYR 0.019 0.001 TYR C 624 ARG 0.009 0.001 ARG D 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 1514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 507 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 LEU cc_start: 0.8391 (mm) cc_final: 0.8151 (mm) REVERT: B 77 TYR cc_start: 0.7852 (m-80) cc_final: 0.7477 (m-80) REVERT: B 82 GLU cc_start: 0.8246 (tt0) cc_final: 0.8013 (tt0) REVERT: B 108 ILE cc_start: 0.8037 (mt) cc_final: 0.7646 (tt) REVERT: B 124 ARG cc_start: 0.8553 (ttt-90) cc_final: 0.7928 (ttt-90) REVERT: B 128 LYS cc_start: 0.8539 (mttt) cc_final: 0.8326 (mttt) REVERT: B 132 PHE cc_start: 0.6812 (m-10) cc_final: 0.6286 (m-10) REVERT: A 237 ASP cc_start: 0.8417 (m-30) cc_final: 0.7834 (t0) REVERT: A 270 ASP cc_start: 0.6965 (t70) cc_final: 0.6641 (t0) REVERT: A 288 ILE cc_start: 0.8672 (mp) cc_final: 0.8431 (mp) REVERT: A 291 MET cc_start: 0.8221 (ttt) cc_final: 0.7793 (ptm) REVERT: A 304 MET cc_start: 0.4500 (tpt) cc_final: 0.3883 (tpt) REVERT: A 315 LYS cc_start: 0.8063 (mmtm) cc_final: 0.7696 (mttt) REVERT: A 332 ASN cc_start: 0.7590 (t0) cc_final: 0.7049 (t0) REVERT: A 337 ARG cc_start: 0.8145 (ttm170) cc_final: 0.7185 (ttp80) REVERT: A 338 ARG cc_start: 0.7782 (mmm-85) cc_final: 0.7227 (mmm-85) REVERT: A 341 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7492 (mt-10) REVERT: A 343 PHE cc_start: 0.8552 (m-80) cc_final: 0.8225 (m-80) REVERT: A 347 ILE cc_start: 0.7704 (mt) cc_final: 0.6904 (tp) REVERT: A 349 TYR cc_start: 0.7511 (t80) cc_final: 0.7295 (t80) REVERT: A 361 LEU cc_start: 0.7201 (tp) cc_final: 0.6937 (tp) REVERT: A 369 VAL cc_start: 0.7920 (t) cc_final: 0.7683 (m) REVERT: A 377 MET cc_start: 0.8213 (mtt) cc_final: 0.7910 (mtp) REVERT: A 392 HIS cc_start: 0.8243 (m90) cc_final: 0.7833 (m90) REVERT: A 398 GLU cc_start: 0.6958 (pm20) cc_final: 0.6386 (pm20) REVERT: A 407 LEU cc_start: 0.8945 (mt) cc_final: 0.8447 (pp) REVERT: A 408 THR cc_start: 0.8225 (m) cc_final: 0.7478 (p) REVERT: A 411 GLU cc_start: 0.7701 (mt-10) cc_final: 0.6871 (mt-10) REVERT: A 432 LEU cc_start: 0.8248 (mt) cc_final: 0.8001 (mt) REVERT: A 446 PHE cc_start: 0.7638 (m-80) cc_final: 0.7431 (m-80) REVERT: A 458 LEU cc_start: 0.8506 (tp) cc_final: 0.8190 (tp) REVERT: A 463 ASP cc_start: 0.7783 (m-30) cc_final: 0.7501 (m-30) REVERT: A 477 PHE cc_start: 0.7596 (m-80) cc_final: 0.7267 (m-80) REVERT: A 478 MET cc_start: 0.7968 (mtp) cc_final: 0.7228 (mtp) REVERT: A 497 ASN cc_start: 0.7404 (m-40) cc_final: 0.7110 (m-40) REVERT: A 499 ILE cc_start: 0.7787 (tp) cc_final: 0.7254 (tp) REVERT: A 501 MET cc_start: 0.7017 (mtt) cc_final: 0.6645 (mmt) REVERT: A 504 GLU cc_start: 0.7873 (mm-30) cc_final: 0.6996 (mm-30) REVERT: A 505 ARG cc_start: 0.8060 (mtt90) cc_final: 0.7362 (mtt90) REVERT: A 506 ARG cc_start: 0.7816 (mtt90) cc_final: 0.7174 (mtt180) REVERT: A 507 ILE cc_start: 0.8496 (mt) cc_final: 0.7996 (mt) REVERT: A 515 GLN cc_start: 0.7417 (tm-30) cc_final: 0.7207 (tm-30) REVERT: A 522 TYR cc_start: 0.7602 (m-80) cc_final: 0.6508 (m-80) REVERT: A 533 ILE cc_start: 0.8518 (pt) cc_final: 0.8094 (mp) REVERT: A 543 ILE cc_start: 0.8550 (mt) cc_final: 0.7644 (mt) REVERT: A 545 MET cc_start: 0.7421 (mtm) cc_final: 0.7116 (mtm) REVERT: A 550 ASP cc_start: 0.7214 (p0) cc_final: 0.6959 (p0) REVERT: A 553 LYS cc_start: 0.8127 (tppp) cc_final: 0.7766 (ttmm) REVERT: A 555 LEU cc_start: 0.8539 (tp) cc_final: 0.8282 (pp) REVERT: A 576 GLN cc_start: 0.7913 (tp40) cc_final: 0.7400 (tp40) REVERT: A 593 ASP cc_start: 0.7525 (t0) cc_final: 0.7218 (t0) REVERT: A 619 LEU cc_start: 0.8693 (tp) cc_final: 0.8454 (tp) REVERT: A 626 ASN cc_start: 0.7968 (m110) cc_final: 0.7642 (m110) REVERT: A 635 MET cc_start: 0.7606 (mpp) cc_final: 0.7074 (mpp) REVERT: A 642 MET cc_start: 0.8055 (mmp) cc_final: 0.7654 (mmp) REVERT: A 651 LEU cc_start: 0.8414 (mt) cc_final: 0.7929 (mt) REVERT: A 658 LEU cc_start: 0.8003 (tp) cc_final: 0.7745 (tp) REVERT: A 659 TYR cc_start: 0.8620 (t80) cc_final: 0.8141 (t80) REVERT: A 660 GLN cc_start: 0.7930 (pp30) cc_final: 0.7216 (pp30) REVERT: A 663 LYS cc_start: 0.8183 (ptmm) cc_final: 0.7517 (mptt) REVERT: A 667 GLU cc_start: 0.8215 (pp20) cc_final: 0.7883 (pp20) REVERT: A 711 LYS cc_start: 0.9224 (mmtt) cc_final: 0.8760 (mmtm) REVERT: A 712 GLU cc_start: 0.8795 (tt0) cc_final: 0.8584 (tt0) REVERT: A 716 LEU cc_start: 0.8773 (mt) cc_final: 0.8268 (pp) REVERT: A 717 TYR cc_start: 0.8590 (t80) cc_final: 0.8117 (t80) REVERT: A 720 TYR cc_start: 0.7325 (t80) cc_final: 0.6891 (t80) REVERT: A 727 GLU cc_start: 0.7556 (pm20) cc_final: 0.7294 (pm20) REVERT: A 735 ARG cc_start: 0.7789 (ttm170) cc_final: 0.7501 (ttm170) REVERT: A 743 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7508 (mm-30) REVERT: A 750 PHE cc_start: 0.7504 (m-80) cc_final: 0.7171 (m-80) REVERT: A 754 GLU cc_start: 0.8425 (mt-10) cc_final: 0.7889 (mp0) REVERT: A 756 GLU cc_start: 0.7561 (tp30) cc_final: 0.7140 (tp30) REVERT: A 763 ARG cc_start: 0.6932 (tpp80) cc_final: 0.6704 (tpp-160) REVERT: A 806 LEU cc_start: 0.8319 (mt) cc_final: 0.7943 (mt) REVERT: A 822 LYS cc_start: 0.8198 (mptt) cc_final: 0.7984 (mmtm) REVERT: A 855 LYS cc_start: 0.8829 (tttt) cc_final: 0.7962 (ttpp) REVERT: D 22 LEU cc_start: 0.8362 (mm) cc_final: 0.8035 (mm) REVERT: D 47 ARG cc_start: 0.7602 (mmm160) cc_final: 0.6502 (mmm160) REVERT: D 65 ASN cc_start: 0.7276 (m-40) cc_final: 0.6953 (m-40) REVERT: D 77 TYR cc_start: 0.7891 (m-80) cc_final: 0.7435 (m-80) REVERT: D 114 GLN cc_start: 0.7367 (mp10) cc_final: 0.7159 (mp10) REVERT: D 132 PHE cc_start: 0.7148 (m-80) cc_final: 0.6304 (m-80) REVERT: D 138 ARG cc_start: 0.7038 (ptt-90) cc_final: 0.6198 (ptt-90) REVERT: C 130 GLU cc_start: 0.8504 (pt0) cc_final: 0.7581 (pm20) REVERT: C 138 GLU cc_start: 0.8455 (mp0) cc_final: 0.8220 (mm-30) REVERT: C 237 ASP cc_start: 0.8299 (m-30) cc_final: 0.7838 (t70) REVERT: C 287 PHE cc_start: 0.6793 (m-80) cc_final: 0.6189 (m-80) REVERT: C 291 MET cc_start: 0.8281 (ttt) cc_final: 0.7579 (ttt) REVERT: C 304 MET cc_start: 0.4741 (tpt) cc_final: 0.4433 (tpt) REVERT: C 315 LYS cc_start: 0.8095 (mtmm) cc_final: 0.7456 (mttt) REVERT: C 328 TRP cc_start: 0.6314 (m100) cc_final: 0.6024 (m100) REVERT: C 332 ASN cc_start: 0.7985 (t0) cc_final: 0.7301 (t0) REVERT: C 336 ILE cc_start: 0.8277 (mt) cc_final: 0.8035 (mt) REVERT: C 337 ARG cc_start: 0.7884 (ptt90) cc_final: 0.7610 (ttp80) REVERT: C 338 ARG cc_start: 0.7760 (mmm-85) cc_final: 0.7076 (mmm160) REVERT: C 341 GLU cc_start: 0.8177 (pm20) cc_final: 0.7479 (pm20) REVERT: C 344 GLN cc_start: 0.8094 (tp-100) cc_final: 0.7199 (tp-100) REVERT: C 347 ILE cc_start: 0.7634 (mt) cc_final: 0.7289 (mt) REVERT: C 349 TYR cc_start: 0.7596 (t80) cc_final: 0.7254 (t80) REVERT: C 376 LYS cc_start: 0.8651 (ttpt) cc_final: 0.8021 (tppt) REVERT: C 377 MET cc_start: 0.8622 (mtt) cc_final: 0.8357 (mtp) REVERT: C 392 HIS cc_start: 0.7993 (m-70) cc_final: 0.7430 (m-70) REVERT: C 407 LEU cc_start: 0.8990 (mt) cc_final: 0.8665 (pp) REVERT: C 410 GLN cc_start: 0.8085 (mm-40) cc_final: 0.7188 (mm-40) REVERT: C 447 GLU cc_start: 0.7688 (mp0) cc_final: 0.7381 (tp30) REVERT: C 450 ILE cc_start: 0.8134 (mt) cc_final: 0.6989 (mt) REVERT: C 459 GLU cc_start: 0.6603 (mp0) cc_final: 0.6380 (mp0) REVERT: C 478 MET cc_start: 0.7830 (mtp) cc_final: 0.7394 (mtp) REVERT: C 482 PHE cc_start: 0.7966 (p90) cc_final: 0.7642 (p90) REVERT: C 496 ASP cc_start: 0.6785 (t70) cc_final: 0.6473 (t70) REVERT: C 499 ILE cc_start: 0.7787 (tp) cc_final: 0.7539 (tp) REVERT: C 501 MET cc_start: 0.7055 (mmp) cc_final: 0.6792 (mmp) REVERT: C 504 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7175 (mm-30) REVERT: C 506 ARG cc_start: 0.7863 (mtt90) cc_final: 0.7150 (mtt90) REVERT: C 507 ILE cc_start: 0.8362 (mt) cc_final: 0.7920 (mt) REVERT: C 530 ASP cc_start: 0.7687 (p0) cc_final: 0.7350 (p0) REVERT: C 541 GLU cc_start: 0.8085 (tt0) cc_final: 0.7067 (tt0) REVERT: C 542 MET cc_start: 0.7645 (tpp) cc_final: 0.7034 (tpp) REVERT: C 543 ILE cc_start: 0.8637 (mt) cc_final: 0.8364 (mt) REVERT: C 545 MET cc_start: 0.7504 (mtm) cc_final: 0.7069 (mtm) REVERT: C 555 LEU cc_start: 0.8212 (tp) cc_final: 0.7892 (tp) REVERT: C 576 GLN cc_start: 0.7356 (tm-30) cc_final: 0.6766 (tm-30) REVERT: C 577 LEU cc_start: 0.8629 (mt) cc_final: 0.8194 (pp) REVERT: C 581 GLU cc_start: 0.7699 (pp20) cc_final: 0.7437 (pp20) REVERT: C 617 ILE cc_start: 0.8396 (mm) cc_final: 0.8080 (mm) REVERT: C 621 LEU cc_start: 0.8042 (mm) cc_final: 0.7450 (mm) REVERT: C 625 ASN cc_start: 0.7968 (m-40) cc_final: 0.7550 (m110) REVERT: C 626 ASN cc_start: 0.7968 (m110) cc_final: 0.7460 (m110) REVERT: C 635 MET cc_start: 0.7675 (mpp) cc_final: 0.7155 (mpp) REVERT: C 640 LYS cc_start: 0.7782 (mtpp) cc_final: 0.7394 (mtpp) REVERT: C 641 LEU cc_start: 0.8280 (mt) cc_final: 0.7924 (mm) REVERT: C 642 MET cc_start: 0.7797 (mmp) cc_final: 0.7473 (mmp) REVERT: C 648 PHE cc_start: 0.8593 (p90) cc_final: 0.8150 (p90) REVERT: C 651 LEU cc_start: 0.8559 (mt) cc_final: 0.7970 (mt) REVERT: C 659 TYR cc_start: 0.8736 (t80) cc_final: 0.8242 (t80) REVERT: C 660 GLN cc_start: 0.8411 (mm-40) cc_final: 0.8196 (mm-40) REVERT: C 663 LYS cc_start: 0.8050 (ptmm) cc_final: 0.7583 (mmtt) REVERT: C 666 LEU cc_start: 0.8600 (mm) cc_final: 0.8388 (mm) REVERT: C 667 GLU cc_start: 0.7874 (pp20) cc_final: 0.7527 (pp20) REVERT: C 711 LYS cc_start: 0.9269 (mmtt) cc_final: 0.8775 (mmtm) REVERT: C 712 GLU cc_start: 0.8779 (tt0) cc_final: 0.8063 (tt0) REVERT: C 716 LEU cc_start: 0.8859 (mt) cc_final: 0.8587 (mp) REVERT: C 717 TYR cc_start: 0.8569 (t80) cc_final: 0.8189 (t80) REVERT: C 719 ASP cc_start: 0.7897 (m-30) cc_final: 0.7599 (m-30) REVERT: C 720 TYR cc_start: 0.7517 (t80) cc_final: 0.7093 (t80) REVERT: C 730 PHE cc_start: 0.7365 (t80) cc_final: 0.6932 (t80) REVERT: C 738 HIS cc_start: 0.7595 (t70) cc_final: 0.6897 (t70) REVERT: C 739 MET cc_start: 0.7353 (ptm) cc_final: 0.7089 (ptm) REVERT: C 743 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7366 (mm-30) REVERT: C 747 LYS cc_start: 0.8953 (mtpt) cc_final: 0.8710 (mmmt) REVERT: C 748 TYR cc_start: 0.6812 (t80) cc_final: 0.6544 (t80) REVERT: C 756 GLU cc_start: 0.6994 (tp30) cc_final: 0.6464 (tp30) REVERT: C 757 LEU cc_start: 0.7809 (mm) cc_final: 0.7608 (mm) REVERT: C 788 ARG cc_start: 0.8326 (ptp-110) cc_final: 0.7931 (ptp-110) REVERT: C 792 GLU cc_start: 0.8285 (mm-30) cc_final: 0.8036 (mm-30) REVERT: C 801 GLN cc_start: 0.8342 (mp10) cc_final: 0.7984 (mp10) REVERT: C 805 PHE cc_start: 0.8228 (t80) cc_final: 0.7854 (t80) REVERT: C 806 LEU cc_start: 0.8233 (mt) cc_final: 0.7690 (mt) REVERT: C 855 LYS cc_start: 0.8728 (tttt) cc_final: 0.8305 (mmtt) outliers start: 0 outliers final: 0 residues processed: 507 average time/residue: 0.3330 time to fit residues: 229.9255 Evaluate side-chains 489 residues out of total 1514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 489 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 145 optimal weight: 10.0000 chunk 87 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 137 optimal weight: 0.2980 chunk 144 optimal weight: 0.7980 chunk 95 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 ASN C 455 ASN ** C 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 554 GLN ** C 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 632 HIS ** C 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 738 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.6580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13522 Z= 0.178 Angle : 0.661 9.433 18260 Z= 0.333 Chirality : 0.044 0.233 2014 Planarity : 0.005 0.075 2372 Dihedral : 5.073 25.821 1806 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.21), residues: 1610 helix: -0.39 (0.18), residues: 796 sheet: -2.64 (0.58), residues: 72 loop : -0.94 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.004 TRP D 139 HIS 0.007 0.001 HIS C 655 PHE 0.029 0.002 PHE C 633 TYR 0.018 0.001 TYR A 494 ARG 0.008 0.001 ARG A 763 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 1514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 503 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 LEU cc_start: 0.8170 (mm) cc_final: 0.7895 (mm) REVERT: B 77 TYR cc_start: 0.7890 (m-80) cc_final: 0.7435 (m-80) REVERT: B 88 TYR cc_start: 0.6868 (p90) cc_final: 0.6640 (p90) REVERT: B 108 ILE cc_start: 0.8033 (mt) cc_final: 0.7630 (tt) REVERT: B 124 ARG cc_start: 0.8598 (ttt-90) cc_final: 0.7552 (ttt-90) REVERT: B 132 PHE cc_start: 0.6890 (m-10) cc_final: 0.6331 (m-10) REVERT: A 130 GLU cc_start: 0.8469 (pt0) cc_final: 0.7410 (pm20) REVERT: A 237 ASP cc_start: 0.8431 (m-30) cc_final: 0.7888 (t0) REVERT: A 270 ASP cc_start: 0.7028 (t70) cc_final: 0.6742 (t0) REVERT: A 287 PHE cc_start: 0.6974 (m-80) cc_final: 0.6772 (m-80) REVERT: A 291 MET cc_start: 0.8184 (ttt) cc_final: 0.7781 (ttp) REVERT: A 304 MET cc_start: 0.4500 (tpt) cc_final: 0.3885 (tpt) REVERT: A 315 LYS cc_start: 0.8053 (mmtm) cc_final: 0.7717 (mttt) REVERT: A 326 ARG cc_start: 0.7620 (mtm-85) cc_final: 0.7418 (mtm-85) REVERT: A 331 TYR cc_start: 0.6591 (m-10) cc_final: 0.6313 (m-10) REVERT: A 337 ARG cc_start: 0.8206 (ttm170) cc_final: 0.7351 (ttp80) REVERT: A 341 GLU cc_start: 0.8428 (mt-10) cc_final: 0.7863 (mt-10) REVERT: A 343 PHE cc_start: 0.8466 (m-80) cc_final: 0.8116 (m-80) REVERT: A 347 ILE cc_start: 0.7746 (mt) cc_final: 0.6999 (tp) REVERT: A 349 TYR cc_start: 0.7489 (t80) cc_final: 0.7284 (t80) REVERT: A 377 MET cc_start: 0.8142 (mtt) cc_final: 0.7900 (mtp) REVERT: A 392 HIS cc_start: 0.8235 (m90) cc_final: 0.7804 (m90) REVERT: A 398 GLU cc_start: 0.6895 (pm20) cc_final: 0.6366 (pm20) REVERT: A 407 LEU cc_start: 0.8961 (mt) cc_final: 0.8425 (pp) REVERT: A 408 THR cc_start: 0.8193 (m) cc_final: 0.7316 (m) REVERT: A 410 GLN cc_start: 0.8069 (mp-120) cc_final: 0.7783 (mm-40) REVERT: A 411 GLU cc_start: 0.7670 (mt-10) cc_final: 0.6826 (mt-10) REVERT: A 432 LEU cc_start: 0.8240 (mt) cc_final: 0.7995 (mt) REVERT: A 447 GLU cc_start: 0.7770 (tp30) cc_final: 0.7092 (tp30) REVERT: A 449 PHE cc_start: 0.7159 (m-10) cc_final: 0.6874 (m-10) REVERT: A 450 ILE cc_start: 0.8244 (mt) cc_final: 0.7693 (mt) REVERT: A 458 LEU cc_start: 0.8505 (tp) cc_final: 0.8162 (tp) REVERT: A 463 ASP cc_start: 0.7835 (m-30) cc_final: 0.7378 (m-30) REVERT: A 477 PHE cc_start: 0.7644 (m-80) cc_final: 0.7310 (m-80) REVERT: A 478 MET cc_start: 0.7984 (mtp) cc_final: 0.7415 (mtp) REVERT: A 497 ASN cc_start: 0.7335 (m-40) cc_final: 0.7075 (m-40) REVERT: A 499 ILE cc_start: 0.7767 (tp) cc_final: 0.7416 (tp) REVERT: A 502 TYR cc_start: 0.6879 (m-10) cc_final: 0.6642 (m-10) REVERT: A 504 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7013 (mm-30) REVERT: A 505 ARG cc_start: 0.8074 (mtt90) cc_final: 0.7341 (mtt90) REVERT: A 507 ILE cc_start: 0.8493 (mt) cc_final: 0.7879 (mt) REVERT: A 515 GLN cc_start: 0.7486 (tm-30) cc_final: 0.7274 (tm-30) REVERT: A 522 TYR cc_start: 0.7570 (m-80) cc_final: 0.6536 (m-80) REVERT: A 533 ILE cc_start: 0.8528 (pt) cc_final: 0.7940 (mp) REVERT: A 543 ILE cc_start: 0.8499 (mt) cc_final: 0.7613 (mt) REVERT: A 545 MET cc_start: 0.7360 (mtm) cc_final: 0.7037 (mtm) REVERT: A 550 ASP cc_start: 0.7190 (p0) cc_final: 0.6972 (p0) REVERT: A 553 LYS cc_start: 0.8103 (tppp) cc_final: 0.7872 (ttmm) REVERT: A 560 GLU cc_start: 0.6496 (pm20) cc_final: 0.6274 (mm-30) REVERT: A 572 LYS cc_start: 0.7861 (tptt) cc_final: 0.7175 (tptp) REVERT: A 593 ASP cc_start: 0.7517 (t0) cc_final: 0.7221 (t0) REVERT: A 619 LEU cc_start: 0.8678 (tp) cc_final: 0.8435 (tp) REVERT: A 621 LEU cc_start: 0.8077 (mp) cc_final: 0.7384 (mt) REVERT: A 626 ASN cc_start: 0.8008 (m110) cc_final: 0.7706 (m110) REVERT: A 635 MET cc_start: 0.7564 (mpp) cc_final: 0.6955 (mpp) REVERT: A 642 MET cc_start: 0.7976 (mmp) cc_final: 0.7674 (mmp) REVERT: A 651 LEU cc_start: 0.8431 (mt) cc_final: 0.7971 (mt) REVERT: A 658 LEU cc_start: 0.7946 (tp) cc_final: 0.7713 (tp) REVERT: A 659 TYR cc_start: 0.8582 (t80) cc_final: 0.8257 (t80) REVERT: A 660 GLN cc_start: 0.7873 (pp30) cc_final: 0.7146 (pp30) REVERT: A 663 LYS cc_start: 0.8169 (ptmm) cc_final: 0.7597 (mmtt) REVERT: A 667 GLU cc_start: 0.8199 (pp20) cc_final: 0.7866 (pp20) REVERT: A 711 LYS cc_start: 0.9259 (mmtt) cc_final: 0.8792 (mmtm) REVERT: A 712 GLU cc_start: 0.8753 (tt0) cc_final: 0.8526 (tt0) REVERT: A 716 LEU cc_start: 0.8802 (mt) cc_final: 0.8319 (pp) REVERT: A 717 TYR cc_start: 0.8601 (t80) cc_final: 0.8230 (t80) REVERT: A 727 GLU cc_start: 0.7540 (pm20) cc_final: 0.7301 (pm20) REVERT: A 728 LYS cc_start: 0.8214 (ttpt) cc_final: 0.7561 (tmtt) REVERT: A 735 ARG cc_start: 0.7756 (ttm170) cc_final: 0.7396 (ttm170) REVERT: A 743 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7526 (mm-30) REVERT: A 750 PHE cc_start: 0.7497 (m-80) cc_final: 0.7266 (m-80) REVERT: A 754 GLU cc_start: 0.8397 (mt-10) cc_final: 0.7905 (mp0) REVERT: A 756 GLU cc_start: 0.7557 (tp30) cc_final: 0.7152 (tp30) REVERT: A 763 ARG cc_start: 0.6944 (tpp80) cc_final: 0.6708 (tpp-160) REVERT: A 788 ARG cc_start: 0.8441 (ppt170) cc_final: 0.7563 (ttp80) REVERT: A 806 LEU cc_start: 0.8269 (mt) cc_final: 0.7844 (mt) REVERT: A 822 LYS cc_start: 0.8151 (mptt) cc_final: 0.7915 (mmtm) REVERT: A 855 LYS cc_start: 0.8691 (tttt) cc_final: 0.8269 (mmtt) REVERT: D 22 LEU cc_start: 0.8310 (mm) cc_final: 0.7968 (mm) REVERT: D 47 ARG cc_start: 0.7602 (mmm160) cc_final: 0.6509 (mmm160) REVERT: D 62 ARG cc_start: 0.6361 (mmt-90) cc_final: 0.6100 (mmt-90) REVERT: D 65 ASN cc_start: 0.7179 (m-40) cc_final: 0.6978 (m-40) REVERT: D 77 TYR cc_start: 0.7889 (m-80) cc_final: 0.7071 (m-80) REVERT: D 98 GLN cc_start: 0.8413 (mp10) cc_final: 0.8165 (mp10) REVERT: D 114 GLN cc_start: 0.7341 (mp10) cc_final: 0.7137 (mp10) REVERT: D 132 PHE cc_start: 0.7113 (m-80) cc_final: 0.6370 (m-80) REVERT: D 138 ARG cc_start: 0.6966 (ptt-90) cc_final: 0.6063 (ptt-90) REVERT: C 138 GLU cc_start: 0.8457 (mp0) cc_final: 0.8200 (mm-30) REVERT: C 237 ASP cc_start: 0.8247 (m-30) cc_final: 0.7880 (t0) REVERT: C 304 MET cc_start: 0.4773 (tpt) cc_final: 0.4438 (tpt) REVERT: C 315 LYS cc_start: 0.8058 (mtmm) cc_final: 0.7471 (mttt) REVERT: C 332 ASN cc_start: 0.7905 (t0) cc_final: 0.7276 (t0) REVERT: C 336 ILE cc_start: 0.8229 (mt) cc_final: 0.7994 (mt) REVERT: C 337 ARG cc_start: 0.7946 (ptt90) cc_final: 0.7553 (ttp80) REVERT: C 341 GLU cc_start: 0.7991 (pm20) cc_final: 0.7584 (pm20) REVERT: C 347 ILE cc_start: 0.7404 (mt) cc_final: 0.7061 (mt) REVERT: C 349 TYR cc_start: 0.7546 (t80) cc_final: 0.7226 (t80) REVERT: C 376 LYS cc_start: 0.8631 (ttpt) cc_final: 0.7966 (tppt) REVERT: C 392 HIS cc_start: 0.8067 (m-70) cc_final: 0.7496 (m-70) REVERT: C 407 LEU cc_start: 0.8982 (mt) cc_final: 0.8639 (pp) REVERT: C 410 GLN cc_start: 0.8510 (mm-40) cc_final: 0.7178 (mm-40) REVERT: C 447 GLU cc_start: 0.7701 (mp0) cc_final: 0.7375 (tp30) REVERT: C 450 ILE cc_start: 0.8183 (mt) cc_final: 0.7105 (mt) REVERT: C 455 ASN cc_start: 0.7747 (m110) cc_final: 0.7540 (m-40) REVERT: C 478 MET cc_start: 0.7861 (mtp) cc_final: 0.7422 (mtp) REVERT: C 482 PHE cc_start: 0.7896 (p90) cc_final: 0.7509 (p90) REVERT: C 493 LEU cc_start: 0.7175 (tp) cc_final: 0.6813 (tp) REVERT: C 499 ILE cc_start: 0.7772 (tp) cc_final: 0.7515 (tp) REVERT: C 501 MET cc_start: 0.6871 (mmp) cc_final: 0.6386 (mmp) REVERT: C 504 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7220 (mm-30) REVERT: C 505 ARG cc_start: 0.8265 (mtt90) cc_final: 0.7804 (mtt90) REVERT: C 506 ARG cc_start: 0.7871 (mtt90) cc_final: 0.7144 (mtt90) REVERT: C 507 ILE cc_start: 0.8372 (mt) cc_final: 0.7958 (mt) REVERT: C 531 HIS cc_start: 0.7212 (m90) cc_final: 0.6930 (m90) REVERT: C 539 ARG cc_start: 0.7722 (tpp80) cc_final: 0.7482 (ttm170) REVERT: C 542 MET cc_start: 0.7618 (tpp) cc_final: 0.7163 (tpp) REVERT: C 543 ILE cc_start: 0.8602 (mt) cc_final: 0.8324 (mt) REVERT: C 545 MET cc_start: 0.7544 (mtm) cc_final: 0.7278 (mtm) REVERT: C 553 LYS cc_start: 0.7832 (tppp) cc_final: 0.7549 (ttmm) REVERT: C 555 LEU cc_start: 0.8215 (tp) cc_final: 0.7931 (tp) REVERT: C 576 GLN cc_start: 0.7295 (tm-30) cc_final: 0.6681 (tm-30) REVERT: C 577 LEU cc_start: 0.8631 (mt) cc_final: 0.8275 (mt) REVERT: C 581 GLU cc_start: 0.7658 (pp20) cc_final: 0.7357 (pp20) REVERT: C 617 ILE cc_start: 0.8430 (mm) cc_final: 0.8213 (mm) REVERT: C 621 LEU cc_start: 0.8003 (mm) cc_final: 0.7486 (mm) REVERT: C 625 ASN cc_start: 0.7877 (m-40) cc_final: 0.7519 (m-40) REVERT: C 626 ASN cc_start: 0.7809 (m110) cc_final: 0.7370 (m110) REVERT: C 635 MET cc_start: 0.7659 (mpp) cc_final: 0.7139 (mpp) REVERT: C 640 LYS cc_start: 0.7766 (mtpp) cc_final: 0.7088 (mtpp) REVERT: C 641 LEU cc_start: 0.8304 (mt) cc_final: 0.7917 (mm) REVERT: C 642 MET cc_start: 0.7822 (mmp) cc_final: 0.7487 (mmp) REVERT: C 648 PHE cc_start: 0.8569 (p90) cc_final: 0.8195 (p90) REVERT: C 651 LEU cc_start: 0.8563 (mt) cc_final: 0.7984 (mt) REVERT: C 659 TYR cc_start: 0.8721 (t80) cc_final: 0.8267 (t80) REVERT: C 660 GLN cc_start: 0.8426 (mm-40) cc_final: 0.8171 (mm-40) REVERT: C 663 LYS cc_start: 0.8073 (ptmm) cc_final: 0.7575 (mmtt) REVERT: C 667 GLU cc_start: 0.7865 (pp20) cc_final: 0.7511 (pp20) REVERT: C 681 GLN cc_start: 0.6964 (tm-30) cc_final: 0.6038 (tm-30) REVERT: C 707 ASN cc_start: 0.8076 (p0) cc_final: 0.7804 (p0) REVERT: C 711 LYS cc_start: 0.9254 (mmtt) cc_final: 0.8721 (mmtm) REVERT: C 712 GLU cc_start: 0.8795 (tt0) cc_final: 0.8269 (tt0) REVERT: C 716 LEU cc_start: 0.8858 (mt) cc_final: 0.8255 (tp) REVERT: C 717 TYR cc_start: 0.8590 (t80) cc_final: 0.8261 (t80) REVERT: C 719 ASP cc_start: 0.7875 (m-30) cc_final: 0.7589 (m-30) REVERT: C 720 TYR cc_start: 0.7519 (t80) cc_final: 0.7088 (t80) REVERT: C 730 PHE cc_start: 0.7404 (t80) cc_final: 0.6709 (t80) REVERT: C 739 MET cc_start: 0.7371 (ptm) cc_final: 0.7095 (ptm) REVERT: C 743 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7325 (mm-30) REVERT: C 747 LYS cc_start: 0.8953 (mtpt) cc_final: 0.8707 (mmmt) REVERT: C 748 TYR cc_start: 0.6841 (t80) cc_final: 0.6562 (t80) REVERT: C 751 ARG cc_start: 0.7557 (ttm-80) cc_final: 0.7056 (ttm110) REVERT: C 754 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7765 (mt-10) REVERT: C 756 GLU cc_start: 0.6924 (tp30) cc_final: 0.6405 (tp30) REVERT: C 788 ARG cc_start: 0.8295 (ptp-110) cc_final: 0.7898 (ptp-110) REVERT: C 792 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7978 (mm-30) REVERT: C 805 PHE cc_start: 0.8175 (t80) cc_final: 0.7828 (t80) REVERT: C 806 LEU cc_start: 0.8180 (mt) cc_final: 0.7630 (mt) REVERT: C 855 LYS cc_start: 0.8736 (tttt) cc_final: 0.8350 (mmtt) outliers start: 0 outliers final: 0 residues processed: 503 average time/residue: 0.3237 time to fit residues: 222.1585 Evaluate side-chains 478 residues out of total 1514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 478 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 72 optimal weight: 0.0470 chunk 106 optimal weight: 0.7980 chunk 161 optimal weight: 0.9990 chunk 148 optimal weight: 0.7980 chunk 128 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 99 optimal weight: 0.0970 chunk 78 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 HIS C 382 ASN ** C 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 554 GLN C 576 GLN ** C 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.6794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13522 Z= 0.173 Angle : 0.658 9.837 18260 Z= 0.331 Chirality : 0.044 0.203 2014 Planarity : 0.004 0.064 2372 Dihedral : 5.016 23.913 1806 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.21), residues: 1610 helix: -0.41 (0.18), residues: 806 sheet: -2.50 (0.59), residues: 72 loop : -0.96 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP D 139 HIS 0.010 0.001 HIS C 297 PHE 0.028 0.001 PHE A 633 TYR 0.051 0.002 TYR C 301 ARG 0.007 0.000 ARG A 763 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 1514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 496 time to evaluate : 1.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 18 LYS cc_start: 0.7739 (mmtm) cc_final: 0.7246 (mmmm) REVERT: B 22 LEU cc_start: 0.7967 (mm) cc_final: 0.7695 (mm) REVERT: B 77 TYR cc_start: 0.7908 (m-80) cc_final: 0.7453 (m-80) REVERT: B 88 TYR cc_start: 0.6878 (p90) cc_final: 0.6638 (p90) REVERT: B 98 GLN cc_start: 0.8759 (mp10) cc_final: 0.8468 (mp10) REVERT: B 108 ILE cc_start: 0.8064 (mt) cc_final: 0.7638 (tt) REVERT: B 128 LYS cc_start: 0.8391 (mtmm) cc_final: 0.8099 (pttt) REVERT: B 132 PHE cc_start: 0.6874 (m-10) cc_final: 0.6294 (m-10) REVERT: A 130 GLU cc_start: 0.8413 (pt0) cc_final: 0.7398 (pm20) REVERT: A 237 ASP cc_start: 0.8417 (m-30) cc_final: 0.7834 (t0) REVERT: A 260 LEU cc_start: 0.8896 (mm) cc_final: 0.8676 (pp) REVERT: A 270 ASP cc_start: 0.7019 (t70) cc_final: 0.6793 (t0) REVERT: A 304 MET cc_start: 0.4465 (tpt) cc_final: 0.3862 (tpt) REVERT: A 315 LYS cc_start: 0.8023 (mmtm) cc_final: 0.7686 (mttt) REVERT: A 326 ARG cc_start: 0.7624 (mtm-85) cc_final: 0.7394 (mtm-85) REVERT: A 331 TYR cc_start: 0.6546 (m-10) cc_final: 0.6269 (m-10) REVERT: A 332 ASN cc_start: 0.7551 (t0) cc_final: 0.7058 (t0) REVERT: A 337 ARG cc_start: 0.8178 (ttm170) cc_final: 0.7357 (ttp80) REVERT: A 341 GLU cc_start: 0.8430 (mt-10) cc_final: 0.7887 (mt-10) REVERT: A 347 ILE cc_start: 0.7856 (mt) cc_final: 0.7129 (tp) REVERT: A 349 TYR cc_start: 0.7478 (t80) cc_final: 0.7266 (t80) REVERT: A 379 TYR cc_start: 0.7521 (t80) cc_final: 0.7195 (t80) REVERT: A 392 HIS cc_start: 0.8209 (m90) cc_final: 0.7796 (m90) REVERT: A 407 LEU cc_start: 0.8937 (mt) cc_final: 0.8430 (pp) REVERT: A 408 THR cc_start: 0.8183 (m) cc_final: 0.7461 (p) REVERT: A 410 GLN cc_start: 0.8096 (mp-120) cc_final: 0.7821 (mm-40) REVERT: A 411 GLU cc_start: 0.7689 (mt-10) cc_final: 0.6819 (mt-10) REVERT: A 432 LEU cc_start: 0.8223 (mt) cc_final: 0.7988 (mt) REVERT: A 446 PHE cc_start: 0.7635 (m-80) cc_final: 0.7332 (m-80) REVERT: A 447 GLU cc_start: 0.7688 (tp30) cc_final: 0.7012 (tp30) REVERT: A 449 PHE cc_start: 0.7108 (m-10) cc_final: 0.6794 (m-10) REVERT: A 450 ILE cc_start: 0.8083 (mt) cc_final: 0.7518 (mt) REVERT: A 458 LEU cc_start: 0.8497 (tp) cc_final: 0.8111 (tp) REVERT: A 463 ASP cc_start: 0.7847 (m-30) cc_final: 0.7356 (m-30) REVERT: A 477 PHE cc_start: 0.7582 (m-80) cc_final: 0.7288 (m-80) REVERT: A 478 MET cc_start: 0.7912 (mtp) cc_final: 0.6921 (mtp) REVERT: A 499 ILE cc_start: 0.7711 (tp) cc_final: 0.7452 (tp) REVERT: A 504 GLU cc_start: 0.7772 (mm-30) cc_final: 0.6985 (mm-30) REVERT: A 505 ARG cc_start: 0.8085 (mtt90) cc_final: 0.7371 (mtt90) REVERT: A 506 ARG cc_start: 0.7844 (mtt90) cc_final: 0.7226 (mtt90) REVERT: A 507 ILE cc_start: 0.8513 (mt) cc_final: 0.7846 (mt) REVERT: A 515 GLN cc_start: 0.7541 (tm-30) cc_final: 0.7339 (tm-30) REVERT: A 533 ILE cc_start: 0.8490 (pt) cc_final: 0.8072 (mp) REVERT: A 543 ILE cc_start: 0.8470 (mt) cc_final: 0.7529 (mt) REVERT: A 545 MET cc_start: 0.7334 (mtm) cc_final: 0.6955 (mtm) REVERT: A 555 LEU cc_start: 0.8313 (tp) cc_final: 0.8092 (pp) REVERT: A 560 GLU cc_start: 0.6410 (pm20) cc_final: 0.6159 (mm-30) REVERT: A 572 LYS cc_start: 0.7760 (tptt) cc_final: 0.7280 (tptp) REVERT: A 581 GLU cc_start: 0.7886 (pp20) cc_final: 0.7551 (pp20) REVERT: A 593 ASP cc_start: 0.7548 (t0) cc_final: 0.7250 (t0) REVERT: A 619 LEU cc_start: 0.8650 (tp) cc_final: 0.8424 (tp) REVERT: A 625 ASN cc_start: 0.7841 (m110) cc_final: 0.7519 (m-40) REVERT: A 626 ASN cc_start: 0.7965 (m110) cc_final: 0.7689 (m110) REVERT: A 635 MET cc_start: 0.7540 (mpp) cc_final: 0.6954 (mpp) REVERT: A 642 MET cc_start: 0.7985 (mmp) cc_final: 0.7701 (mmp) REVERT: A 651 LEU cc_start: 0.8455 (mt) cc_final: 0.8002 (mt) REVERT: A 659 TYR cc_start: 0.8595 (t80) cc_final: 0.8256 (t80) REVERT: A 660 GLN cc_start: 0.7873 (pp30) cc_final: 0.7100 (pp30) REVERT: A 663 LYS cc_start: 0.8170 (ptmm) cc_final: 0.7602 (mptt) REVERT: A 667 GLU cc_start: 0.8179 (pp20) cc_final: 0.7851 (pp20) REVERT: A 711 LYS cc_start: 0.9256 (mmtt) cc_final: 0.8793 (mmtm) REVERT: A 712 GLU cc_start: 0.8768 (tt0) cc_final: 0.8510 (tt0) REVERT: A 716 LEU cc_start: 0.8795 (mt) cc_final: 0.8300 (pp) REVERT: A 717 TYR cc_start: 0.8642 (t80) cc_final: 0.8107 (t80) REVERT: A 727 GLU cc_start: 0.7522 (pm20) cc_final: 0.7289 (pm20) REVERT: A 728 LYS cc_start: 0.8202 (ttpt) cc_final: 0.7552 (tmtt) REVERT: A 743 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7534 (mm-30) REVERT: A 748 TYR cc_start: 0.6761 (t80) cc_final: 0.6486 (t80) REVERT: A 756 GLU cc_start: 0.7558 (tp30) cc_final: 0.7112 (tp30) REVERT: A 788 ARG cc_start: 0.8486 (ppt170) cc_final: 0.7612 (ttp80) REVERT: A 806 LEU cc_start: 0.8248 (mt) cc_final: 0.7928 (mt) REVERT: A 855 LYS cc_start: 0.8715 (tttt) cc_final: 0.8251 (tptt) REVERT: D 22 LEU cc_start: 0.8375 (mm) cc_final: 0.8034 (mm) REVERT: D 47 ARG cc_start: 0.7583 (mmm160) cc_final: 0.6515 (mmm160) REVERT: D 62 ARG cc_start: 0.6250 (mmt-90) cc_final: 0.6025 (mmt-90) REVERT: D 77 TYR cc_start: 0.7916 (m-80) cc_final: 0.7419 (m-80) REVERT: D 80 ILE cc_start: 0.8344 (mm) cc_final: 0.8093 (mm) REVERT: D 108 ILE cc_start: 0.8042 (mt) cc_final: 0.7838 (mt) REVERT: D 114 GLN cc_start: 0.7343 (mp10) cc_final: 0.7099 (mp10) REVERT: D 132 PHE cc_start: 0.7203 (m-80) cc_final: 0.6371 (m-80) REVERT: D 138 ARG cc_start: 0.6988 (ptt-90) cc_final: 0.6140 (ptt-90) REVERT: C 130 GLU cc_start: 0.8459 (pt0) cc_final: 0.7562 (pm20) REVERT: C 138 GLU cc_start: 0.8484 (mp0) cc_final: 0.8183 (mm-30) REVERT: C 260 LEU cc_start: 0.8691 (mm) cc_final: 0.8355 (pp) REVERT: C 288 ILE cc_start: 0.8790 (tt) cc_final: 0.8553 (pt) REVERT: C 304 MET cc_start: 0.4575 (tpt) cc_final: 0.4258 (tpt) REVERT: C 309 PHE cc_start: 0.7490 (t80) cc_final: 0.7266 (t80) REVERT: C 315 LYS cc_start: 0.8165 (mtmm) cc_final: 0.7848 (mttm) REVERT: C 326 ARG cc_start: 0.7713 (mtt180) cc_final: 0.7470 (mtt180) REVERT: C 330 LYS cc_start: 0.8531 (mmmt) cc_final: 0.8173 (mmtm) REVERT: C 332 ASN cc_start: 0.7854 (t0) cc_final: 0.7164 (t0) REVERT: C 336 ILE cc_start: 0.8335 (mt) cc_final: 0.7872 (mt) REVERT: C 337 ARG cc_start: 0.8039 (ptt90) cc_final: 0.7524 (ttp80) REVERT: C 341 GLU cc_start: 0.7924 (pm20) cc_final: 0.7474 (pm20) REVERT: C 347 ILE cc_start: 0.7447 (mt) cc_final: 0.7154 (mt) REVERT: C 349 TYR cc_start: 0.7567 (t80) cc_final: 0.7224 (t80) REVERT: C 376 LYS cc_start: 0.8607 (ttpt) cc_final: 0.7892 (tppt) REVERT: C 389 ASP cc_start: 0.6745 (t0) cc_final: 0.6246 (t0) REVERT: C 392 HIS cc_start: 0.8011 (m-70) cc_final: 0.7004 (m-70) REVERT: C 407 LEU cc_start: 0.9040 (mt) cc_final: 0.8617 (pp) REVERT: C 410 GLN cc_start: 0.8491 (mm-40) cc_final: 0.7203 (mm-40) REVERT: C 447 GLU cc_start: 0.7688 (mp0) cc_final: 0.7366 (tp30) REVERT: C 450 ILE cc_start: 0.8134 (mt) cc_final: 0.7009 (mt) REVERT: C 478 MET cc_start: 0.7867 (mtp) cc_final: 0.7327 (mtp) REVERT: C 482 PHE cc_start: 0.7894 (p90) cc_final: 0.7543 (p90) REVERT: C 493 LEU cc_start: 0.7138 (tp) cc_final: 0.6855 (tp) REVERT: C 497 ASN cc_start: 0.7109 (m-40) cc_final: 0.6828 (m-40) REVERT: C 499 ILE cc_start: 0.7795 (tp) cc_final: 0.7427 (tp) REVERT: C 501 MET cc_start: 0.6775 (mmp) cc_final: 0.6519 (mmp) REVERT: C 504 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7259 (mm-30) REVERT: C 505 ARG cc_start: 0.8274 (mtt90) cc_final: 0.7791 (mtt90) REVERT: C 507 ILE cc_start: 0.8374 (mt) cc_final: 0.7943 (mt) REVERT: C 530 ASP cc_start: 0.7606 (p0) cc_final: 0.7349 (p0) REVERT: C 539 ARG cc_start: 0.7712 (tpp80) cc_final: 0.7510 (ttt180) REVERT: C 542 MET cc_start: 0.7583 (tpp) cc_final: 0.7118 (tpp) REVERT: C 543 ILE cc_start: 0.8550 (mt) cc_final: 0.8300 (mt) REVERT: C 545 MET cc_start: 0.7551 (mtm) cc_final: 0.7298 (mtm) REVERT: C 555 LEU cc_start: 0.8139 (tp) cc_final: 0.7805 (tp) REVERT: C 576 GLN cc_start: 0.7137 (tm130) cc_final: 0.6525 (tm130) REVERT: C 577 LEU cc_start: 0.8636 (mt) cc_final: 0.8251 (pp) REVERT: C 581 GLU cc_start: 0.7747 (pp20) cc_final: 0.7225 (pp20) REVERT: C 617 ILE cc_start: 0.8406 (mm) cc_final: 0.8193 (mm) REVERT: C 635 MET cc_start: 0.7662 (mpp) cc_final: 0.7093 (mpp) REVERT: C 640 LYS cc_start: 0.7749 (mtpp) cc_final: 0.7037 (mtpp) REVERT: C 641 LEU cc_start: 0.8345 (mt) cc_final: 0.7909 (mm) REVERT: C 642 MET cc_start: 0.7897 (mmp) cc_final: 0.7480 (mmp) REVERT: C 648 PHE cc_start: 0.8555 (p90) cc_final: 0.8128 (p90) REVERT: C 651 LEU cc_start: 0.8525 (mt) cc_final: 0.7939 (mt) REVERT: C 659 TYR cc_start: 0.8705 (t80) cc_final: 0.8117 (t80) REVERT: C 660 GLN cc_start: 0.8438 (mm-40) cc_final: 0.7831 (mm-40) REVERT: C 663 LYS cc_start: 0.8081 (ptmm) cc_final: 0.7769 (mmtt) REVERT: C 667 GLU cc_start: 0.7883 (pp20) cc_final: 0.7539 (pp20) REVERT: C 681 GLN cc_start: 0.6802 (tm-30) cc_final: 0.5783 (tm-30) REVERT: C 693 MET cc_start: 0.6259 (tpt) cc_final: 0.5955 (tpt) REVERT: C 711 LYS cc_start: 0.9235 (mmtt) cc_final: 0.8730 (mmtm) REVERT: C 712 GLU cc_start: 0.8807 (tt0) cc_final: 0.8285 (tt0) REVERT: C 716 LEU cc_start: 0.8863 (mt) cc_final: 0.8250 (tp) REVERT: C 717 TYR cc_start: 0.8604 (t80) cc_final: 0.8277 (t80) REVERT: C 719 ASP cc_start: 0.7891 (m-30) cc_final: 0.7606 (m-30) REVERT: C 720 TYR cc_start: 0.7490 (t80) cc_final: 0.7048 (t80) REVERT: C 730 PHE cc_start: 0.7400 (t80) cc_final: 0.6664 (t80) REVERT: C 738 HIS cc_start: 0.7730 (t-90) cc_final: 0.7078 (t-170) REVERT: C 739 MET cc_start: 0.7319 (ptm) cc_final: 0.7065 (ptm) REVERT: C 743 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7254 (mm-30) REVERT: C 747 LYS cc_start: 0.8944 (mtpt) cc_final: 0.8688 (mmmt) REVERT: C 748 TYR cc_start: 0.6795 (t80) cc_final: 0.6562 (t80) REVERT: C 754 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8021 (mt-10) REVERT: C 756 GLU cc_start: 0.6899 (tp30) cc_final: 0.6438 (tp30) REVERT: C 766 ASP cc_start: 0.7878 (p0) cc_final: 0.7429 (p0) REVERT: C 788 ARG cc_start: 0.8294 (ptp-110) cc_final: 0.7908 (ptp-110) REVERT: C 806 LEU cc_start: 0.8201 (mt) cc_final: 0.7792 (mt) REVERT: C 855 LYS cc_start: 0.8736 (tttt) cc_final: 0.8354 (mmtt) outliers start: 0 outliers final: 0 residues processed: 496 average time/residue: 0.3069 time to fit residues: 205.2306 Evaluate side-chains 468 residues out of total 1514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 468 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 18 optimal weight: 0.0970 chunk 35 optimal weight: 0.0670 chunk 128 optimal weight: 0.4980 chunk 53 optimal weight: 0.4980 chunk 132 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 23 optimal weight: 0.1980 chunk 113 optimal weight: 0.5980 overall best weight: 0.2716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 HIS C 382 ASN C 392 HIS C 455 ASN ** C 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.144356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.117700 restraints weight = 29167.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.122293 restraints weight = 17618.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.125667 restraints weight = 12111.577| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.6992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13522 Z= 0.162 Angle : 0.653 9.929 18260 Z= 0.329 Chirality : 0.044 0.184 2014 Planarity : 0.004 0.053 2372 Dihedral : 4.905 22.421 1806 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.21), residues: 1610 helix: -0.25 (0.18), residues: 794 sheet: -2.57 (0.61), residues: 68 loop : -1.07 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 328 HIS 0.007 0.001 HIS C 655 PHE 0.024 0.001 PHE C 309 TYR 0.018 0.001 TYR C 624 ARG 0.007 0.000 ARG C 294 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4092.40 seconds wall clock time: 72 minutes 49.62 seconds (4369.62 seconds total)