Starting phenix.real_space_refine on Sat May 17 21:58:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vml_43359/05_2025/8vml_43359_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vml_43359/05_2025/8vml_43359.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vml_43359/05_2025/8vml_43359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vml_43359/05_2025/8vml_43359.map" model { file = "/net/cci-nas-00/data/ceres_data/8vml_43359/05_2025/8vml_43359_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vml_43359/05_2025/8vml_43359_neut.cif" } resolution = 3.5 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= 0.000 sd= 0.033 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 1328 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: 4 Type Number sf(0) Gaussians S 94 5.16 5 C 9472 2.51 5 N 2687 2.21 5 O 2694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14947 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3340 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 19, 'TRANS': 419} Chain breaks: 7 Unresolved non-hydrogen bonds: 294 Unresolved non-hydrogen angles: 356 Unresolved non-hydrogen dihedrals: 234 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 9, 'ASN:plan1': 9, 'HIS:plan': 1, 'GLU:plan': 16, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 184 Chain: "B" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 290 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 36} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'M3L:plan-1': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 4278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4278 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PTRANS': 33, 'TRANS': 572} Chain breaks: 2 Unresolved non-hydrogen bonds: 604 Unresolved non-hydrogen angles: 753 Unresolved non-hydrogen dihedrals: 486 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 6, 'ASP:plan': 15, 'PHE:plan': 6, 'GLU:plan': 27, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 372 Chain: "I" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 156 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 19} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 2874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2874 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 12, 'TRANS': 349} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "N" Number of atoms: 3080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3080 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 22, 'TRANS': 372} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 42 Chain: "P" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 929 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 7, 'TRANS': 118} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Time building chain proxies: 10.17, per 1000 atoms: 0.68 Number of scatterers: 14947 At special positions: 0 Unit cell: (159.96, 116.96, 101.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 94 16.00 O 2694 8.00 N 2687 7.00 C 9472 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 - 3.00 Amino acid : True - 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: 4.02 Conformation dependent library (CDL) restraints added in 2.3 seconds 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3808 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 24 sheets defined 25.3% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 83 through 105 removed outlier: 3.947A pdb=" N LYS A 92 " --> pdb=" O GLN A 88 " (cutoff:3.500A) Proline residue: A 93 - end of helix removed outlier: 3.917A pdb=" N ILE A 96 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 119 removed outlier: 6.253A pdb=" N THR A 116 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N TYR A 117 " --> pdb=" O THR A 114 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER A 119 " --> pdb=" O THR A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 147 removed outlier: 4.046A pdb=" N ASP A 135 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASP A 136 " --> pdb=" O PHE A 132 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N MET A 137 " --> pdb=" O LYS A 133 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET A 144 " --> pdb=" O LYS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 459 through 470 Processing helix chain 'A' and resid 502 through 508 Processing helix chain 'A' and resid 539 through 543 Processing helix chain 'A' and resid 589 through 601 removed outlier: 3.621A pdb=" N ILE A 597 " --> pdb=" O ARG A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 625 removed outlier: 4.150A pdb=" N VAL A 613 " --> pdb=" O GLY A 609 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS A 624 " --> pdb=" O HIS A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 630 No H-bonds generated for 'chain 'A' and resid 628 through 630' Processing helix chain 'A' and resid 631 through 651 removed outlier: 3.820A pdb=" N MET A 637 " --> pdb=" O ASN A 633 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N GLN A 645 " --> pdb=" O GLU A 641 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N LYS A 646 " --> pdb=" O ASN A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 666 Processing helix chain 'A' and resid 670 through 682 removed outlier: 4.558A pdb=" N ASP A 675 " --> pdb=" O ILE A 671 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N LYS A 676 " --> pdb=" O MET A 672 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL A 678 " --> pdb=" O ILE A 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 151 removed outlier: 4.122A pdb=" N SER B 148 " --> pdb=" O ILE B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 166 Processing helix chain 'C' and resid 18 through 61 removed outlier: 4.165A pdb=" N LEU C 29 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU C 54 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 143 removed outlier: 3.628A pdb=" N ASP C 142 " --> pdb=" O VAL C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 154 removed outlier: 3.954A pdb=" N GLU C 147 " --> pdb=" O GLY C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 178 removed outlier: 3.573A pdb=" N VAL C 172 " --> pdb=" O ASP C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 231 Processing helix chain 'C' and resid 236 through 250 removed outlier: 4.021A pdb=" N LEU C 240 " --> pdb=" O THR C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 284 removed outlier: 4.935A pdb=" N SER C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N PHE C 281 " --> pdb=" O SER C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 339 removed outlier: 4.082A pdb=" N ALA C 336 " --> pdb=" O LYS C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 448 removed outlier: 4.007A pdb=" N GLY C 445 " --> pdb=" O ARG C 441 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR C 446 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR C 447 " --> pdb=" O LEU C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 458 removed outlier: 3.540A pdb=" N ILE C 454 " --> pdb=" O ASN C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 473 Processing helix chain 'C' and resid 474 through 477 Processing helix chain 'C' and resid 491 through 495 removed outlier: 3.530A pdb=" N LYS C 495 " --> pdb=" O LYS C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 510 removed outlier: 3.855A pdb=" N ALA C 500 " --> pdb=" O HIS C 496 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS C 510 " --> pdb=" O ILE C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 540 Processing helix chain 'C' and resid 571 through 576 Processing helix chain 'C' and resid 604 through 609 removed outlier: 3.595A pdb=" N ARG C 608 " --> pdb=" O CYS C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 661 removed outlier: 3.549A pdb=" N ARG C 654 " --> pdb=" O GLU C 650 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL C 657 " --> pdb=" O ARG C 653 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR C 661 " --> pdb=" O VAL C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 687 Processing helix chain 'C' and resid 729 through 737 Processing helix chain 'L' and resid 128 through 130 No H-bonds generated for 'chain 'L' and resid 128 through 130' Processing helix chain 'L' and resid 267 through 278 Processing helix chain 'L' and resid 339 through 343 removed outlier: 3.584A pdb=" N ILE L 343 " --> pdb=" O ILE L 340 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 28 removed outlier: 3.695A pdb=" N ASN N 18 " --> pdb=" O GLU N 14 " (cutoff:3.500A) Processing helix chain 'N' and resid 155 through 157 No H-bonds generated for 'chain 'N' and resid 155 through 157' Processing helix chain 'N' and resid 355 through 362 Processing helix chain 'N' and resid 406 through 409 Processing helix chain 'P' and resid 191 through 210 removed outlier: 3.744A pdb=" N ALA P 197 " --> pdb=" O GLN P 193 " (cutoff:3.500A) Processing helix chain 'P' and resid 257 through 259 No H-bonds generated for 'chain 'P' and resid 257 through 259' Processing helix chain 'P' and resid 270 through 272 No H-bonds generated for 'chain 'P' and resid 270 through 272' Processing helix chain 'P' and resid 276 through 285 removed outlier: 3.695A pdb=" N LEU P 279 " --> pdb=" O THR P 276 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU P 280 " --> pdb=" O ALA P 277 " (cutoff:3.500A) Proline residue: P 282 - end of helix removed outlier: 3.525A pdb=" N TYR P 285 " --> pdb=" O PRO P 282 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 230 through 233 removed outlier: 4.127A pdb=" N ALA A 318 " --> pdb=" O ILE P 227 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE P 227 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL P 226 " --> pdb=" O HIS P 242 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N HIS P 242 " --> pdb=" O VAL P 226 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA P 228 " --> pdb=" O LEU P 240 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 230 through 233 removed outlier: 4.127A pdb=" N ALA A 318 " --> pdb=" O ILE P 227 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE P 227 " --> pdb=" O ALA A 318 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 203 through 211 removed outlier: 3.978A pdb=" N THR A 208 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N VAL A 186 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LYS A 210 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU A 184 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLU A 185 " --> pdb=" O PHE A 252 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N PHE A 252 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A 187 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU A 250 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL A 189 " --> pdb=" O TYR A 248 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N TYR A 248 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL A 191 " --> pdb=" O LYS A 246 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 439 through 443 removed outlier: 6.214A pdb=" N ARG A 427 " --> pdb=" O ALA A 485 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ILE A 487 " --> pdb=" O ARG A 427 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N PHE A 429 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N VAL A 489 " --> pdb=" O PHE A 429 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLN A 431 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N ILE A 491 " --> pdb=" O GLN A 431 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N LEU A 433 " --> pdb=" O ILE A 491 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 558 through 560 removed outlier: 3.633A pdb=" N ILE A 525 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR N 37 " --> pdb=" O HIS A 527 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 529 " --> pdb=" O VAL N 35 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL N 35 " --> pdb=" O LEU A 529 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU N 34 " --> pdb=" O GLN N 403 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE N 390 " --> pdb=" O TRP N 402 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 94 through 97 removed outlier: 4.062A pdb=" N GLN C 94 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N CYS L 84 " --> pdb=" O ASP L 438 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ASP L 438 " --> pdb=" O CYS L 84 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN L 86 " --> pdb=" O ARG L 436 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER L 433 " --> pdb=" O CYS L 429 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL L 428 " --> pdb=" O GLN L 415 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N GLN L 415 " --> pdb=" O VAL L 428 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 114 through 115 removed outlier: 5.919A pdb=" N SER C 114 " --> pdb=" O GLY C 681 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 120 through 121 removed outlier: 6.535A pdb=" N PHE C 120 " --> pdb=" O ILE C 645 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N SER C 647 " --> pdb=" O PHE C 120 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 285 through 286 Processing sheet with id=AB1, first strand: chain 'C' and resid 614 through 618 Processing sheet with id=AB2, first strand: chain 'C' and resid 637 through 640 removed outlier: 6.780A pdb=" N ILE C 710 " --> pdb=" O ILE C 638 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLU C 640 " --> pdb=" O ILE C 708 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ILE C 708 " --> pdb=" O GLU C 640 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 688 through 689 removed outlier: 6.388A pdb=" N ASN C 688 " --> pdb=" O PHE C 724 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'L' and resid 100 through 101 removed outlier: 4.578A pdb=" N LEU L 111 " --> pdb=" O CYS L 126 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN L 136 " --> pdb=" O LEU L 123 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLU L 125 " --> pdb=" O LEU L 134 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N LEU L 134 " --> pdb=" O GLU L 125 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 147 through 154 removed outlier: 3.827A pdb=" N THR L 149 " --> pdb=" O ALA L 166 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA L 166 " --> pdb=" O THR L 149 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS L 184 " --> pdb=" O ILE L 174 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASN L 176 " --> pdb=" O CYS L 182 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N CYS L 182 " --> pdb=" O ASN L 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 193 through 198 removed outlier: 3.801A pdb=" N GLU L 195 " --> pdb=" O VAL L 209 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU L 215 " --> pdb=" O ILE L 228 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE L 228 " --> pdb=" O LEU L 215 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU L 217 " --> pdb=" O VAL L 226 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR L 224 " --> pdb=" O ASN L 219 " (cutoff:3.500A) removed outlier: 9.511A pdb=" N GLN L 292 " --> pdb=" O THR L 224 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL L 226 " --> pdb=" O GLN L 292 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ILE L 294 " --> pdb=" O VAL L 226 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE L 228 " --> pdb=" O ILE L 294 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 239 through 244 removed outlier: 4.137A pdb=" N PHE L 299 " --> pdb=" O LEU L 262 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 312 through 315 removed outlier: 3.953A pdb=" N SER L 323 " --> pdb=" O ALA L 327 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ALA L 327 " --> pdb=" O SER L 323 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS L 332 " --> pdb=" O ILE L 352 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ILE L 352 " --> pdb=" O LYS L 332 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 368 through 370 Processing sheet with id=AC1, first strand: chain 'N' and resid 48 through 49 removed outlier: 3.907A pdb=" N GLN N 48 " --> pdb=" O VAL N 67 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ASN N 77 " --> pdb=" O ASN N 122 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ASN N 122 " --> pdb=" O ASN N 77 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU N 79 " --> pdb=" O LYS N 120 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LYS N 120 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE N 81 " --> pdb=" O GLU N 118 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU N 116 " --> pdb=" O SER N 83 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 129 through 133 removed outlier: 4.042A pdb=" N ARG N 129 " --> pdb=" O LYS N 143 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ILE N 139 " --> pdb=" O MET N 133 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 180 through 185 Processing sheet with id=AC4, first strand: chain 'N' and resid 230 through 235 removed outlier: 6.702A pdb=" N VAL N 246 " --> pdb=" O GLU N 231 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL N 233 " --> pdb=" O GLY N 244 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLY N 244 " --> pdb=" O VAL N 233 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TRP N 235 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N LEU N 242 " --> pdb=" O TRP N 235 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA N 247 " --> pdb=" O LYS N 251 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LYS N 251 " --> pdb=" O ALA N 247 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 276 through 281 Processing sheet with id=AC6, first strand: chain 'N' and resid 320 through 325 removed outlier: 6.891A pdb=" N SER N 336 " --> pdb=" O PHE N 321 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL N 323 " --> pdb=" O ALA N 334 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ALA N 334 " --> pdb=" O VAL N 323 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N TRP N 325 " --> pdb=" O ILE N 332 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ILE N 332 " --> pdb=" O TRP N 325 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU N 333 " --> pdb=" O TRP N 345 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU N 342 " --> pdb=" O HIS N 370 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ASP N 346 " --> pdb=" O LEU N 366 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N LEU N 366 " --> pdb=" O ASP N 346 " (cutoff:3.500A) 515 hydrogen bonds defined for protein. 1422 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: 6.10 Time building geometry restraints manager: 4.70 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: 4973 1.34 - 1.46: 3470 1.46 - 1.58: 6738 1.58 - 1.70: 0 1.70 - 1.81: 129 Bond restraints: 15310 Sorted by residual: bond pdb=" N ARG B 108 " pdb=" CA ARG B 108 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 bond pdb=" N LYS C 17 " pdb=" CA LYS C 17 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" N LYS N 4 " pdb=" CA LYS N 4 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 bond pdb=" CB ARG C 741 " pdb=" CG ARG C 741 " ideal model delta sigma weight residual 1.520 1.572 -0.052 3.00e-02 1.11e+03 3.01e+00 bond pdb=" N ALA A 81 " pdb=" CA ALA A 81 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 ... (remaining 15305 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 20365 1.74 - 3.49: 395 3.49 - 5.23: 59 5.23 - 6.97: 6 6.97 - 8.71: 4 Bond angle restraints: 20829 Sorted by residual: angle pdb=" CB LYS C 612 " pdb=" CG LYS C 612 " pdb=" CD LYS C 612 " ideal model delta sigma weight residual 111.30 120.01 -8.71 2.30e+00 1.89e-01 1.44e+01 angle pdb=" CA ARG C 741 " pdb=" CB ARG C 741 " pdb=" CG ARG C 741 " ideal model delta sigma weight residual 114.10 121.60 -7.50 2.00e+00 2.50e-01 1.41e+01 angle pdb=" CG ARG C 741 " pdb=" CD ARG C 741 " pdb=" NE ARG C 741 " ideal model delta sigma weight residual 112.00 119.98 -7.98 2.20e+00 2.07e-01 1.32e+01 angle pdb=" N THR B 159 " pdb=" CA THR B 159 " pdb=" CB THR B 159 " ideal model delta sigma weight residual 114.17 110.66 3.51 1.14e+00 7.69e-01 9.49e+00 angle pdb=" CB ARG C 741 " pdb=" CG ARG C 741 " pdb=" CD ARG C 741 " ideal model delta sigma weight residual 111.30 118.36 -7.06 2.30e+00 1.89e-01 9.43e+00 ... (remaining 20824 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 8236 17.76 - 35.53: 713 35.53 - 53.29: 149 53.29 - 71.05: 27 71.05 - 88.81: 7 Dihedral angle restraints: 9132 sinusoidal: 3298 harmonic: 5834 Sorted by residual: dihedral pdb=" CA ALA C 576 " pdb=" C ALA C 576 " pdb=" N VAL C 577 " pdb=" CA VAL C 577 " ideal model delta harmonic sigma weight residual -180.00 -159.49 -20.51 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA ASP L 237 " pdb=" C ASP L 237 " pdb=" N GLU L 238 " pdb=" CA GLU L 238 " ideal model delta harmonic sigma weight residual 180.00 161.48 18.52 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ASP C 581 " pdb=" CB ASP C 581 " pdb=" CG ASP C 581 " pdb=" OD1 ASP C 581 " ideal model delta sinusoidal sigma weight residual -30.00 -87.98 57.98 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 9129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1490 0.030 - 0.060: 556 0.060 - 0.091: 134 0.091 - 0.121: 122 0.121 - 0.151: 25 Chirality restraints: 2327 Sorted by residual: chirality pdb=" CA ILE L 171 " pdb=" N ILE L 171 " pdb=" C ILE L 171 " pdb=" CB ILE L 171 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CA ILE N 390 " pdb=" N ILE N 390 " pdb=" C ILE N 390 " pdb=" CB ILE N 390 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.41e-01 chirality pdb=" CA VAL N 246 " pdb=" N VAL N 246 " pdb=" C VAL N 246 " pdb=" CB VAL N 246 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 ... (remaining 2324 not shown) Planarity restraints: 2702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET N 133 " -0.032 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO N 134 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO N 134 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO N 134 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 572 " -0.031 5.00e-02 4.00e+02 4.71e-02 3.55e+00 pdb=" N PRO A 573 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 573 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 573 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 487 " 0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO C 488 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO C 488 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 488 " 0.024 5.00e-02 4.00e+02 ... (remaining 2699 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 61 2.48 - 3.08: 10716 3.08 - 3.69: 21615 3.69 - 4.29: 29867 4.29 - 4.90: 50137 Nonbonded interactions: 112396 Sorted by model distance: nonbonded pdb=" O ARG C 741 " pdb=" NE ARG C 741 " model vdw 1.873 3.120 nonbonded pdb=" OG SER C 112 " pdb=" O ASP L 212 " model vdw 2.005 3.040 nonbonded pdb=" O LEU A 311 " pdb=" OH TYR A 315 " model vdw 2.126 3.040 nonbonded pdb=" O HIS P 187 " pdb=" ND1 HIS P 187 " model vdw 2.135 3.120 nonbonded pdb=" O MET C 41 " pdb=" OG SER C 44 " model vdw 2.187 3.040 ... (remaining 112391 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 9.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.870 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 37.710 Find NCS groups from input model: 0.200 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: 0.010 Load rotamer database and sin/cos tables:3.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5807 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 : 0.003 0.052 15310 Z= 0.130 Angle : 0.617 8.713 20829 Z= 0.351 Chirality : 0.041 0.151 2327 Planarity : 0.004 0.048 2702 Dihedral : 14.245 88.812 5324 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.55 % Allowed : 14.70 % Favored : 84.76 % 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: -1.57 (0.18), residues: 1953 helix: -0.09 (0.26), residues: 408 sheet: -0.61 (0.25), residues: 401 loop : -1.61 (0.17), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 499 HIS 0.004 0.001 HIS A 527 PHE 0.013 0.001 PHE A 164 TYR 0.010 0.001 TYR A 557 ARG 0.006 0.000 ARG L 439 Details of bonding type rmsd hydrogen bonds : bond 0.19140 ( 497) hydrogen bonds : angle 8.20646 ( 1422) covalent geometry : bond 0.00254 (15310) covalent geometry : angle 0.61713 (20829) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 298 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 LYS cc_start: 0.6428 (tttt) cc_final: 0.6083 (tppt) REVERT: A 248 TYR cc_start: 0.7812 (m-80) cc_final: 0.7510 (m-80) REVERT: A 495 TYR cc_start: 0.6564 (t80) cc_final: 0.6295 (t80) REVERT: B 112 GLN cc_start: 0.4793 (mt0) cc_final: 0.4202 (tp40) REVERT: C 90 ASP cc_start: 0.7009 (t0) cc_final: 0.6749 (t0) REVERT: C 156 LYS cc_start: 0.4795 (ttpt) cc_final: 0.4581 (tptt) REVERT: C 264 ILE cc_start: 0.6783 (tt) cc_final: 0.6118 (mm) REVERT: C 290 PHE cc_start: 0.6424 (m-80) cc_final: 0.6092 (m-80) REVERT: C 504 ARG cc_start: 0.7877 (ttm-80) cc_final: 0.7235 (tpt170) REVERT: C 580 CYS cc_start: 0.8099 (m) cc_final: 0.7228 (m) REVERT: L 158 THR cc_start: 0.8083 (p) cc_final: 0.7601 (p) REVERT: L 160 HIS cc_start: 0.7976 (m170) cc_final: 0.7608 (m170) REVERT: L 243 ASP cc_start: 0.7795 (t0) cc_final: 0.7484 (t0) REVERT: L 330 CYS cc_start: 0.8372 (p) cc_final: 0.8011 (m) REVERT: L 337 GLU cc_start: 0.5668 (pt0) cc_final: 0.5431 (tm-30) REVERT: L 376 MET cc_start: 0.6803 (ttp) cc_final: 0.6538 (ttm) REVERT: L 389 TRP cc_start: 0.5721 (m-90) cc_final: 0.5282 (m100) REVERT: N 36 MET cc_start: 0.4744 (mmm) cc_final: 0.4453 (ttm) REVERT: N 233 VAL cc_start: 0.6340 (p) cc_final: 0.6049 (p) REVERT: N 376 LYS cc_start: 0.7098 (tttt) cc_final: 0.6830 (tttp) REVERT: P 216 LYS cc_start: 0.6827 (mttt) cc_final: 0.6247 (tttp) REVERT: P 230 ARG cc_start: 0.3267 (ptt180) cc_final: 0.2985 (tmm-80) REVERT: P 231 LYS cc_start: 0.5224 (ttpp) cc_final: 0.4981 (ttmm) REVERT: P 253 TRP cc_start: 0.4532 (m100) cc_final: 0.4021 (m100) REVERT: P 281 ASP cc_start: 0.7354 (t0) cc_final: 0.6114 (m-30) REVERT: P 286 ARG cc_start: 0.7029 (tpt-90) cc_final: 0.5878 (mtp-110) outliers start: 8 outliers final: 3 residues processed: 300 average time/residue: 0.2689 time to fit residues: 116.5703 Evaluate side-chains 217 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 214 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain L residue 349 ASN Chi-restraints excluded: chain L residue 363 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 6.9990 chunk 148 optimal weight: 0.6980 chunk 82 optimal weight: 7.9990 chunk 50 optimal weight: 0.6980 chunk 100 optimal weight: 0.4980 chunk 79 optimal weight: 9.9990 chunk 153 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 177 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 241 ASN A 527 HIS A 624 HIS C 502 HIS L 374 GLN N 27 ASN P 268 HIS P 283 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.176843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.140612 restraints weight = 25116.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.144313 restraints weight = 14490.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.145162 restraints weight = 9886.067| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15310 Z= 0.128 Angle : 0.616 9.431 20829 Z= 0.318 Chirality : 0.045 0.171 2327 Planarity : 0.004 0.057 2702 Dihedral : 4.358 23.382 2125 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.67 % Allowed : 15.99 % Favored : 81.34 % 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: -1.25 (0.18), residues: 1953 helix: 0.44 (0.25), residues: 423 sheet: -0.34 (0.24), residues: 403 loop : -1.56 (0.17), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP N 205 HIS 0.006 0.001 HIS A 481 PHE 0.012 0.001 PHE C 285 TYR 0.016 0.001 TYR N 154 ARG 0.006 0.001 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.05053 ( 497) hydrogen bonds : angle 5.64342 ( 1422) covalent geometry : bond 0.00264 (15310) covalent geometry : angle 0.61578 (20829) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 235 time to evaluate : 1.640 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: A 299 MET cc_start: 0.3705 (tpt) cc_final: 0.2374 (mmt) REVERT: B 112 GLN cc_start: 0.4951 (mt0) cc_final: 0.4416 (tp40) REVERT: C 90 ASP cc_start: 0.6216 (t0) cc_final: 0.6005 (t0) REVERT: C 156 LYS cc_start: 0.5585 (ttpt) cc_final: 0.5362 (tptt) REVERT: C 504 ARG cc_start: 0.7724 (ttm-80) cc_final: 0.7085 (tpt170) REVERT: C 580 CYS cc_start: 0.7539 (m) cc_final: 0.6645 (m) REVERT: C 737 VAL cc_start: 0.6310 (t) cc_final: 0.6010 (m) REVERT: L 158 THR cc_start: 0.8869 (p) cc_final: 0.8457 (p) REVERT: N 233 VAL cc_start: 0.6634 (p) cc_final: 0.6418 (p) REVERT: N 242 LEU cc_start: 0.5786 (mm) cc_final: 0.5413 (tp) REVERT: N 287 PHE cc_start: 0.4574 (m-80) cc_final: 0.3790 (m-10) REVERT: N 402 TRP cc_start: 0.7234 (p-90) cc_final: 0.7031 (p-90) REVERT: P 216 LYS cc_start: 0.7374 (mttt) cc_final: 0.7111 (tttp) REVERT: P 230 ARG cc_start: 0.3540 (ptt180) cc_final: 0.3114 (tmm-80) REVERT: P 231 LYS cc_start: 0.5738 (ttpp) cc_final: 0.5499 (ttmm) REVERT: P 253 TRP cc_start: 0.5508 (m100) cc_final: 0.4420 (m100) REVERT: P 286 ARG cc_start: 0.7346 (tpt-90) cc_final: 0.6799 (mtp-110) outliers start: 39 outliers final: 29 residues processed: 264 average time/residue: 0.2799 time to fit residues: 107.0083 Evaluate side-chains 222 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 193 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 HIS Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 705 ASP Chi-restraints excluded: chain L residue 128 SER Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 196 LEU Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 405 THR Chi-restraints excluded: chain L residue 424 ILE Chi-restraints excluded: chain L residue 425 LEU Chi-restraints excluded: chain N residue 234 SER Chi-restraints excluded: chain N residue 257 THR Chi-restraints excluded: chain N residue 267 HIS Chi-restraints excluded: chain N residue 348 SER Chi-restraints excluded: chain N residue 391 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 177 optimal weight: 0.8980 chunk 159 optimal weight: 8.9990 chunk 185 optimal weight: 0.0070 chunk 143 optimal weight: 0.6980 chunk 58 optimal weight: 0.3980 chunk 78 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 16 optimal weight: 0.1980 chunk 51 optimal weight: 1.9990 chunk 182 optimal weight: 0.3980 overall best weight: 0.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 548 GLN L 160 HIS N 27 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.177306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.141421 restraints weight = 25134.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.143809 restraints weight = 14416.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.145214 restraints weight = 10210.885| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6530 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15310 Z= 0.108 Angle : 0.561 7.622 20829 Z= 0.290 Chirality : 0.043 0.165 2327 Planarity : 0.004 0.050 2702 Dihedral : 4.212 21.247 2119 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.35 % Allowed : 16.68 % Favored : 79.97 % 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: -0.99 (0.18), residues: 1953 helix: 0.76 (0.25), residues: 417 sheet: -0.19 (0.24), residues: 422 loop : -1.44 (0.18), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP N 205 HIS 0.007 0.001 HIS A 527 PHE 0.027 0.001 PHE C 469 TYR 0.015 0.001 TYR A 495 ARG 0.007 0.000 ARG N 55 Details of bonding type rmsd hydrogen bonds : bond 0.04420 ( 497) hydrogen bonds : angle 5.20154 ( 1422) covalent geometry : bond 0.00221 (15310) covalent geometry : angle 0.56131 (20829) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 208 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.3549 (tpt) cc_final: 0.2428 (mmt) REVERT: A 311 LEU cc_start: 0.5734 (OUTLIER) cc_final: 0.5504 (pp) REVERT: B 112 GLN cc_start: 0.4883 (mt0) cc_final: 0.4370 (tp40) REVERT: C 90 ASP cc_start: 0.6282 (t0) cc_final: 0.6074 (t0) REVERT: C 156 LYS cc_start: 0.5439 (ttpt) cc_final: 0.5213 (tptt) REVERT: C 508 LEU cc_start: 0.6893 (OUTLIER) cc_final: 0.6593 (mt) REVERT: L 133 ARG cc_start: 0.7085 (ttp80) cc_final: 0.6868 (tpt90) REVERT: L 376 MET cc_start: 0.6691 (mtp) cc_final: 0.6343 (ttm) REVERT: N 233 VAL cc_start: 0.6730 (p) cc_final: 0.6477 (p) REVERT: N 242 LEU cc_start: 0.5883 (mm) cc_final: 0.5504 (tp) REVERT: N 287 PHE cc_start: 0.4366 (m-80) cc_final: 0.3637 (m-10) REVERT: P 216 LYS cc_start: 0.7451 (mttt) cc_final: 0.7124 (tttp) REVERT: P 253 TRP cc_start: 0.5584 (m100) cc_final: 0.4436 (m100) REVERT: P 281 ASP cc_start: 0.7757 (t0) cc_final: 0.5823 (m-30) REVERT: P 286 ARG cc_start: 0.7385 (tpt-90) cc_final: 0.6947 (mtp-110) outliers start: 49 outliers final: 33 residues processed: 244 average time/residue: 0.2820 time to fit residues: 99.7167 Evaluate side-chains 222 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 187 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 HIS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 309 VAL Chi-restraints excluded: chain L residue 330 CYS Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 424 ILE Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 144 THR Chi-restraints excluded: chain N residue 224 THR Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 257 THR Chi-restraints excluded: chain N residue 267 HIS Chi-restraints excluded: chain N residue 348 SER Chi-restraints excluded: chain N residue 391 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 50 optimal weight: 4.9990 chunk 5 optimal weight: 0.0000 chunk 127 optimal weight: 2.9990 chunk 157 optimal weight: 8.9990 chunk 165 optimal weight: 0.0980 chunk 46 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 192 optimal weight: 9.9990 chunk 169 optimal weight: 0.1980 chunk 1 optimal weight: 0.8980 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 166 HIS A 527 HIS ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 160 HIS N 27 ASN N 328 HIS N 343 ASN ** N 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.175965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.139915 restraints weight = 25314.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.143312 restraints weight = 15683.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.144275 restraints weight = 10766.157| |-----------------------------------------------------------------------------| r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15310 Z= 0.106 Angle : 0.550 8.010 20829 Z= 0.283 Chirality : 0.043 0.165 2327 Planarity : 0.004 0.047 2702 Dihedral : 4.135 20.757 2119 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.49 % Allowed : 16.61 % Favored : 79.90 % 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: -0.84 (0.18), residues: 1953 helix: 0.93 (0.26), residues: 415 sheet: -0.10 (0.24), residues: 428 loop : -1.37 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP N 205 HIS 0.015 0.001 HIS A 83 PHE 0.015 0.001 PHE C 290 TYR 0.016 0.001 TYR N 154 ARG 0.005 0.000 ARG N 55 Details of bonding type rmsd hydrogen bonds : bond 0.04107 ( 497) hydrogen bonds : angle 4.96503 ( 1422) covalent geometry : bond 0.00219 (15310) covalent geometry : angle 0.54993 (20829) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 203 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.3591 (tpt) cc_final: 0.2749 (tpp) REVERT: A 302 PHE cc_start: 0.7211 (m-80) cc_final: 0.6986 (m-10) REVERT: B 112 GLN cc_start: 0.4917 (mt0) cc_final: 0.4434 (tp40) REVERT: C 508 LEU cc_start: 0.6770 (OUTLIER) cc_final: 0.6434 (mt) REVERT: N 242 LEU cc_start: 0.5997 (mm) cc_final: 0.5637 (tp) REVERT: N 287 PHE cc_start: 0.4268 (m-80) cc_final: 0.3597 (m-10) REVERT: P 216 LYS cc_start: 0.7526 (mttt) cc_final: 0.7129 (tmtt) REVERT: P 253 TRP cc_start: 0.5430 (m100) cc_final: 0.4577 (m100) REVERT: P 259 ARG cc_start: 0.5251 (tpt170) cc_final: 0.3966 (mmm160) REVERT: P 281 ASP cc_start: 0.7723 (t0) cc_final: 0.5856 (m-30) REVERT: P 286 ARG cc_start: 0.7483 (tpt-90) cc_final: 0.6955 (mtp-110) outliers start: 51 outliers final: 39 residues processed: 240 average time/residue: 0.2695 time to fit residues: 95.5381 Evaluate side-chains 226 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 186 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 166 HIS Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 734 LEU Chi-restraints excluded: chain L residue 128 SER Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 160 HIS Chi-restraints excluded: chain L residue 213 HIS Chi-restraints excluded: chain L residue 309 VAL Chi-restraints excluded: chain L residue 330 CYS Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 405 THR Chi-restraints excluded: chain L residue 424 ILE Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 144 THR Chi-restraints excluded: chain N residue 224 THR Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 257 THR Chi-restraints excluded: chain N residue 267 HIS Chi-restraints excluded: chain N residue 273 THR Chi-restraints excluded: chain N residue 348 SER Chi-restraints excluded: chain N residue 391 CYS Chi-restraints excluded: chain N residue 404 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 124 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 146 optimal weight: 0.7980 chunk 11 optimal weight: 40.0000 chunk 15 optimal weight: 7.9990 chunk 102 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 HIS ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 160 HIS L 191 ASN N 27 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.166551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.132224 restraints weight = 26163.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.132446 restraints weight = 15709.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.134340 restraints weight = 12155.749| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15310 Z= 0.193 Angle : 0.687 8.629 20829 Z= 0.361 Chirality : 0.047 0.198 2327 Planarity : 0.005 0.055 2702 Dihedral : 4.828 28.552 2119 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 4.92 % Allowed : 16.13 % Favored : 78.95 % 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: -1.17 (0.18), residues: 1953 helix: 0.72 (0.25), residues: 403 sheet: -0.09 (0.24), residues: 410 loop : -1.67 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 314 HIS 0.037 0.002 HIS A 166 PHE 0.027 0.002 PHE C 724 TYR 0.023 0.002 TYR A 480 ARG 0.006 0.001 ARG P 230 Details of bonding type rmsd hydrogen bonds : bond 0.05537 ( 497) hydrogen bonds : angle 5.25543 ( 1422) covalent geometry : bond 0.00446 (15310) covalent geometry : angle 0.68690 (20829) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 196 time to evaluate : 1.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.3721 (tpt) cc_final: 0.2899 (tpp) REVERT: A 300 THR cc_start: 0.4812 (t) cc_final: 0.4216 (t) REVERT: A 529 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7232 (tt) REVERT: B 143 GLN cc_start: 0.6538 (OUTLIER) cc_final: 0.6245 (mp10) REVERT: C 264 ILE cc_start: 0.6205 (OUTLIER) cc_final: 0.5988 (mp) REVERT: C 496 HIS cc_start: 0.7135 (OUTLIER) cc_final: 0.6833 (t-90) REVERT: C 508 LEU cc_start: 0.6751 (OUTLIER) cc_final: 0.6400 (mt) REVERT: C 654 ARG cc_start: 0.6103 (OUTLIER) cc_final: 0.4877 (mtt90) REVERT: L 252 MET cc_start: 0.8091 (ppp) cc_final: 0.7790 (ppp) REVERT: N 242 LEU cc_start: 0.6293 (mm) cc_final: 0.5971 (tp) REVERT: P 216 LYS cc_start: 0.7869 (mttt) cc_final: 0.7439 (tmtt) REVERT: P 253 TRP cc_start: 0.5958 (m100) cc_final: 0.4940 (m100) REVERT: P 259 ARG cc_start: 0.5467 (tpt170) cc_final: 0.4252 (tpp-160) REVERT: P 274 LYS cc_start: 0.4404 (mmmt) cc_final: 0.3971 (mtpt) REVERT: P 281 ASP cc_start: 0.7916 (t0) cc_final: 0.6098 (m-30) REVERT: P 286 ARG cc_start: 0.7432 (tpt-90) cc_final: 0.6889 (mtp85) outliers start: 72 outliers final: 42 residues processed: 250 average time/residue: 0.2925 time to fit residues: 108.1935 Evaluate side-chains 225 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 177 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 166 HIS Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 496 HIS Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 654 ARG Chi-restraints excluded: chain C residue 734 LEU Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 128 SER Chi-restraints excluded: chain L residue 213 HIS Chi-restraints excluded: chain L residue 309 VAL Chi-restraints excluded: chain L residue 330 CYS Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 405 THR Chi-restraints excluded: chain L residue 424 ILE Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 144 THR Chi-restraints excluded: chain N residue 222 ILE Chi-restraints excluded: chain N residue 224 THR Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 257 THR Chi-restraints excluded: chain N residue 267 HIS Chi-restraints excluded: chain N residue 278 CYS Chi-restraints excluded: chain N residue 303 LEU Chi-restraints excluded: chain N residue 348 SER Chi-restraints excluded: chain N residue 391 CYS Chi-restraints excluded: chain N residue 404 MET Chi-restraints excluded: chain P residue 266 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 16 optimal weight: 8.9990 chunk 188 optimal weight: 9.9990 chunk 12 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 180 optimal weight: 0.7980 chunk 155 optimal weight: 6.9990 chunk 153 optimal weight: 0.0980 chunk 76 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 374 GLN N 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.169752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.135133 restraints weight = 25623.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.136361 restraints weight = 15142.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.137930 restraints weight = 11279.913| |-----------------------------------------------------------------------------| r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15310 Z= 0.115 Angle : 0.572 8.044 20829 Z= 0.296 Chirality : 0.044 0.163 2327 Planarity : 0.004 0.047 2702 Dihedral : 4.417 22.487 2119 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.35 % Allowed : 18.25 % Favored : 78.40 % 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: -0.99 (0.18), residues: 1953 helix: 1.01 (0.26), residues: 402 sheet: -0.03 (0.24), residues: 415 loop : -1.60 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP N 205 HIS 0.014 0.001 HIS A 166 PHE 0.015 0.001 PHE A 302 TYR 0.016 0.001 TYR N 154 ARG 0.010 0.000 ARG N 55 Details of bonding type rmsd hydrogen bonds : bond 0.04325 ( 497) hydrogen bonds : angle 4.89023 ( 1422) covalent geometry : bond 0.00251 (15310) covalent geometry : angle 0.57241 (20829) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 194 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 HIS cc_start: 0.8325 (t-90) cc_final: 0.7867 (m-70) REVERT: A 299 MET cc_start: 0.3782 (tpt) cc_final: 0.3154 (tpp) REVERT: A 300 THR cc_start: 0.4821 (t) cc_final: 0.4329 (t) REVERT: A 529 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.7019 (tt) REVERT: B 112 GLN cc_start: 0.4864 (mt0) cc_final: 0.4271 (tp40) REVERT: B 143 GLN cc_start: 0.6440 (OUTLIER) cc_final: 0.5962 (mm-40) REVERT: C 508 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.6387 (mt) REVERT: C 720 GLU cc_start: 0.6994 (mt-10) cc_final: 0.6790 (mt-10) REVERT: L 133 ARG cc_start: 0.7395 (ttp80) cc_final: 0.7070 (tpt90) REVERT: P 216 LYS cc_start: 0.7874 (mttt) cc_final: 0.7416 (tmtt) REVERT: P 230 ARG cc_start: 0.2695 (ttp-170) cc_final: 0.2438 (ttp-170) REVERT: P 259 ARG cc_start: 0.5474 (tpt170) cc_final: 0.4284 (tpp-160) REVERT: P 274 LYS cc_start: 0.4270 (mmmt) cc_final: 0.4007 (mtpt) REVERT: P 281 ASP cc_start: 0.7817 (t0) cc_final: 0.6035 (m-30) REVERT: P 286 ARG cc_start: 0.7466 (tpt-90) cc_final: 0.6893 (mtp85) outliers start: 49 outliers final: 33 residues processed: 232 average time/residue: 0.2735 time to fit residues: 92.8858 Evaluate side-chains 217 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 181 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain L residue 128 SER Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 213 HIS Chi-restraints excluded: chain L residue 309 VAL Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 144 THR Chi-restraints excluded: chain N residue 224 THR Chi-restraints excluded: chain N residue 257 THR Chi-restraints excluded: chain N residue 267 HIS Chi-restraints excluded: chain N residue 273 THR Chi-restraints excluded: chain N residue 278 CYS Chi-restraints excluded: chain N residue 348 SER Chi-restraints excluded: chain N residue 391 CYS Chi-restraints excluded: chain N residue 404 MET Chi-restraints excluded: chain P residue 266 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 185 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 195 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 chunk 135 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 chunk 146 optimal weight: 0.6980 chunk 42 optimal weight: 0.0770 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 374 GLN L 382 GLN N 27 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.170548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.139030 restraints weight = 25764.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.137792 restraints weight = 17110.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.139456 restraints weight = 12821.227| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15310 Z= 0.115 Angle : 0.574 9.276 20829 Z= 0.295 Chirality : 0.043 0.230 2327 Planarity : 0.004 0.046 2702 Dihedral : 4.250 22.663 2119 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.21 % Allowed : 19.34 % Favored : 77.44 % 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: -0.90 (0.18), residues: 1953 helix: 1.14 (0.26), residues: 404 sheet: 0.00 (0.25), residues: 408 loop : -1.54 (0.17), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP N 205 HIS 0.009 0.001 HIS N 226 PHE 0.037 0.001 PHE A 302 TYR 0.014 0.001 TYR N 154 ARG 0.004 0.000 ARG C 287 Details of bonding type rmsd hydrogen bonds : bond 0.04105 ( 497) hydrogen bonds : angle 4.71588 ( 1422) covalent geometry : bond 0.00250 (15310) covalent geometry : angle 0.57411 (20829) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 189 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 HIS cc_start: 0.8366 (t-90) cc_final: 0.7663 (m-70) REVERT: A 299 MET cc_start: 0.3574 (tpt) cc_final: 0.2952 (tpp) REVERT: A 300 THR cc_start: 0.4833 (t) cc_final: 0.4460 (t) REVERT: A 443 GLU cc_start: 0.5706 (tm-30) cc_final: 0.4982 (tm-30) REVERT: A 529 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6965 (tt) REVERT: B 112 GLN cc_start: 0.4818 (mt0) cc_final: 0.4296 (tp40) REVERT: B 143 GLN cc_start: 0.6388 (OUTLIER) cc_final: 0.6077 (mm-40) REVERT: C 508 LEU cc_start: 0.6675 (OUTLIER) cc_final: 0.6297 (mt) REVERT: C 720 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6675 (mt-10) REVERT: N 55 ARG cc_start: 0.6846 (ttm-80) cc_final: 0.6581 (mtt90) REVERT: N 287 PHE cc_start: 0.4356 (OUTLIER) cc_final: 0.3309 (m-10) REVERT: P 216 LYS cc_start: 0.7850 (mttt) cc_final: 0.7445 (tmtt) REVERT: P 259 ARG cc_start: 0.5497 (tpt170) cc_final: 0.4674 (tpp-160) REVERT: P 281 ASP cc_start: 0.7748 (t0) cc_final: 0.5932 (m-30) REVERT: P 286 ARG cc_start: 0.7527 (tpt-90) cc_final: 0.6922 (mtp85) outliers start: 47 outliers final: 38 residues processed: 227 average time/residue: 0.2579 time to fit residues: 87.0388 Evaluate side-chains 219 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 177 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 734 LEU Chi-restraints excluded: chain L residue 128 SER Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 213 HIS Chi-restraints excluded: chain L residue 309 VAL Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 405 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 144 THR Chi-restraints excluded: chain N residue 222 ILE Chi-restraints excluded: chain N residue 224 THR Chi-restraints excluded: chain N residue 257 THR Chi-restraints excluded: chain N residue 267 HIS Chi-restraints excluded: chain N residue 273 THR Chi-restraints excluded: chain N residue 278 CYS Chi-restraints excluded: chain N residue 287 PHE Chi-restraints excluded: chain N residue 303 LEU Chi-restraints excluded: chain N residue 335 SER Chi-restraints excluded: chain N residue 348 SER Chi-restraints excluded: chain N residue 390 ILE Chi-restraints excluded: chain N residue 391 CYS Chi-restraints excluded: chain N residue 404 MET Chi-restraints excluded: chain P residue 266 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 153 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 170 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 7 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.170140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.137900 restraints weight = 25586.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.138005 restraints weight = 15755.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.139802 restraints weight = 11612.683| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15310 Z= 0.120 Angle : 0.578 8.141 20829 Z= 0.298 Chirality : 0.044 0.204 2327 Planarity : 0.004 0.046 2702 Dihedral : 4.273 22.647 2119 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.55 % Allowed : 19.48 % Favored : 76.97 % 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: -0.88 (0.18), residues: 1953 helix: 1.17 (0.26), residues: 402 sheet: 0.08 (0.25), residues: 406 loop : -1.55 (0.17), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP N 205 HIS 0.006 0.001 HIS N 226 PHE 0.014 0.001 PHE A 302 TYR 0.017 0.001 TYR N 21 ARG 0.006 0.000 ARG C 287 Details of bonding type rmsd hydrogen bonds : bond 0.04112 ( 497) hydrogen bonds : angle 4.71614 ( 1422) covalent geometry : bond 0.00264 (15310) covalent geometry : angle 0.57847 (20829) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 181 time to evaluate : 1.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.3995 (tpt) cc_final: 0.3397 (tpp) REVERT: A 300 THR cc_start: 0.4635 (t) cc_final: 0.4288 (t) REVERT: A 319 MET cc_start: 0.3930 (mmm) cc_final: 0.2924 (mmm) REVERT: B 112 GLN cc_start: 0.4750 (mt0) cc_final: 0.4294 (tp40) REVERT: B 143 GLN cc_start: 0.6105 (OUTLIER) cc_final: 0.5797 (mm-40) REVERT: C 508 LEU cc_start: 0.6655 (OUTLIER) cc_final: 0.6269 (mt) REVERT: C 636 GLU cc_start: 0.5995 (mm-30) cc_final: 0.5777 (mm-30) REVERT: C 654 ARG cc_start: 0.6095 (OUTLIER) cc_final: 0.4882 (mtt90) REVERT: P 216 LYS cc_start: 0.7884 (mttt) cc_final: 0.7463 (tmtt) REVERT: P 259 ARG cc_start: 0.5573 (tpt170) cc_final: 0.4754 (tpp-160) REVERT: P 281 ASP cc_start: 0.7756 (t0) cc_final: 0.5955 (m-30) REVERT: P 286 ARG cc_start: 0.7515 (tpt-90) cc_final: 0.6874 (mtp85) outliers start: 52 outliers final: 37 residues processed: 224 average time/residue: 0.2760 time to fit residues: 92.9197 Evaluate side-chains 214 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 174 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 654 ARG Chi-restraints excluded: chain C residue 734 LEU Chi-restraints excluded: chain L residue 128 SER Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 213 HIS Chi-restraints excluded: chain L residue 309 VAL Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 405 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 144 THR Chi-restraints excluded: chain N residue 222 ILE Chi-restraints excluded: chain N residue 224 THR Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 257 THR Chi-restraints excluded: chain N residue 267 HIS Chi-restraints excluded: chain N residue 287 PHE Chi-restraints excluded: chain N residue 303 LEU Chi-restraints excluded: chain N residue 335 SER Chi-restraints excluded: chain N residue 348 SER Chi-restraints excluded: chain N residue 390 ILE Chi-restraints excluded: chain N residue 391 CYS Chi-restraints excluded: chain P residue 266 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 168 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 137 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 8 optimal weight: 8.9990 chunk 128 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 90 optimal weight: 0.4980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 HIS ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 235 HIS L 374 GLN N 27 ASN N 123 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.170357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.138322 restraints weight = 25490.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.138796 restraints weight = 14856.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.140751 restraints weight = 10886.979| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6713 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15310 Z= 0.114 Angle : 0.581 9.417 20829 Z= 0.297 Chirality : 0.043 0.189 2327 Planarity : 0.004 0.045 2702 Dihedral : 4.209 23.557 2119 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.08 % Allowed : 20.64 % Favored : 76.28 % 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: -0.76 (0.19), residues: 1953 helix: 1.22 (0.26), residues: 402 sheet: 0.17 (0.25), residues: 417 loop : -1.48 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP N 205 HIS 0.007 0.001 HIS N 226 PHE 0.015 0.001 PHE C 290 TYR 0.014 0.001 TYR C 574 ARG 0.004 0.000 ARG C 287 Details of bonding type rmsd hydrogen bonds : bond 0.04011 ( 497) hydrogen bonds : angle 4.64124 ( 1422) covalent geometry : bond 0.00253 (15310) covalent geometry : angle 0.58126 (20829) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 177 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.4227 (tpt) cc_final: 0.3600 (tpp) REVERT: A 300 THR cc_start: 0.4688 (t) cc_final: 0.4396 (t) REVERT: A 319 MET cc_start: 0.3939 (mmm) cc_final: 0.2570 (mmm) REVERT: B 112 GLN cc_start: 0.4679 (mt0) cc_final: 0.4313 (tp40) REVERT: B 143 GLN cc_start: 0.6034 (OUTLIER) cc_final: 0.5753 (mm-40) REVERT: C 508 LEU cc_start: 0.6709 (OUTLIER) cc_final: 0.6277 (mt) REVERT: C 654 ARG cc_start: 0.6012 (OUTLIER) cc_final: 0.4711 (mtt90) REVERT: L 281 ASN cc_start: 0.7835 (t0) cc_final: 0.6729 (p0) REVERT: P 216 LYS cc_start: 0.7884 (mttt) cc_final: 0.7432 (tmtt) REVERT: P 259 ARG cc_start: 0.5590 (tpt170) cc_final: 0.4780 (tpp-160) REVERT: P 281 ASP cc_start: 0.7752 (t0) cc_final: 0.5931 (m-30) REVERT: P 286 ARG cc_start: 0.7532 (tpt-90) cc_final: 0.6859 (mtp85) outliers start: 45 outliers final: 37 residues processed: 215 average time/residue: 0.2543 time to fit residues: 81.6805 Evaluate side-chains 211 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 171 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 161 PHE Chi-restraints excluded: chain A residue 166 HIS Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 654 ARG Chi-restraints excluded: chain C residue 734 LEU Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 213 HIS Chi-restraints excluded: chain L residue 309 VAL Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 405 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 144 THR Chi-restraints excluded: chain N residue 222 ILE Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 257 THR Chi-restraints excluded: chain N residue 267 HIS Chi-restraints excluded: chain N residue 287 PHE Chi-restraints excluded: chain N residue 303 LEU Chi-restraints excluded: chain N residue 335 SER Chi-restraints excluded: chain N residue 348 SER Chi-restraints excluded: chain N residue 391 CYS Chi-restraints excluded: chain P residue 266 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 193 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 171 optimal weight: 0.4980 chunk 5 optimal weight: 0.6980 chunk 42 optimal weight: 0.0030 chunk 70 optimal weight: 0.4980 chunk 160 optimal weight: 0.0170 chunk 71 optimal weight: 0.0980 chunk 112 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 overall best weight: 0.2228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 ASN N 135 GLN ** N 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 397 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.172986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.141528 restraints weight = 25539.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.141774 restraints weight = 14875.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.143622 restraints weight = 10982.331| |-----------------------------------------------------------------------------| r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15310 Z= 0.101 Angle : 0.563 8.407 20829 Z= 0.287 Chirality : 0.043 0.169 2327 Planarity : 0.004 0.060 2702 Dihedral : 4.056 21.854 2119 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.39 % Allowed : 21.46 % Favored : 76.14 % 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: -0.62 (0.19), residues: 1953 helix: 1.30 (0.26), residues: 401 sheet: 0.34 (0.25), residues: 405 loop : -1.39 (0.18), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP N 205 HIS 0.006 0.001 HIS A 166 PHE 0.037 0.001 PHE A 165 TYR 0.019 0.001 TYR N 21 ARG 0.003 0.000 ARG C 287 Details of bonding type rmsd hydrogen bonds : bond 0.03595 ( 497) hydrogen bonds : angle 4.50859 ( 1422) covalent geometry : bond 0.00208 (15310) covalent geometry : angle 0.56253 (20829) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 186 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.4236 (tpt) cc_final: 0.3629 (tpp) REVERT: A 300 THR cc_start: 0.4697 (t) cc_final: 0.4496 (t) REVERT: B 112 GLN cc_start: 0.4619 (mt0) cc_final: 0.4287 (tp40) REVERT: B 143 GLN cc_start: 0.6032 (OUTLIER) cc_final: 0.5802 (mm-40) REVERT: C 508 LEU cc_start: 0.6613 (OUTLIER) cc_final: 0.6223 (mt) REVERT: C 654 ARG cc_start: 0.6000 (OUTLIER) cc_final: 0.4647 (mtt90) REVERT: C 720 GLU cc_start: 0.6857 (mt-10) cc_final: 0.6576 (mt-10) REVERT: N 287 PHE cc_start: 0.4119 (OUTLIER) cc_final: 0.3224 (m-10) REVERT: N 395 GLU cc_start: 0.6186 (pm20) cc_final: 0.4746 (mt-10) REVERT: P 216 LYS cc_start: 0.7772 (mttt) cc_final: 0.7190 (tptm) REVERT: P 259 ARG cc_start: 0.5601 (tpt170) cc_final: 0.4820 (tpp-160) REVERT: P 281 ASP cc_start: 0.7529 (t0) cc_final: 0.5793 (m-30) REVERT: P 286 ARG cc_start: 0.7525 (tpt-90) cc_final: 0.6891 (mtp85) outliers start: 35 outliers final: 27 residues processed: 218 average time/residue: 0.2825 time to fit residues: 90.4633 Evaluate side-chains 206 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 161 PHE Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 654 ARG Chi-restraints excluded: chain C residue 742 GLU Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 213 HIS Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 405 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 144 THR Chi-restraints excluded: chain N residue 257 THR Chi-restraints excluded: chain N residue 267 HIS Chi-restraints excluded: chain N residue 287 PHE Chi-restraints excluded: chain P residue 266 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 178 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 62 optimal weight: 30.0000 chunk 118 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 HIS A 356 GLN ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN L 93 ASN L 374 GLN N 27 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.165781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.133341 restraints weight = 26181.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.133571 restraints weight = 15481.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.135441 restraints weight = 12091.604| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15310 Z= 0.192 Angle : 0.681 8.665 20829 Z= 0.355 Chirality : 0.047 0.216 2327 Planarity : 0.005 0.056 2702 Dihedral : 4.654 26.227 2119 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.87 % Allowed : 21.80 % Favored : 75.32 % 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: -1.00 (0.18), residues: 1953 helix: 0.93 (0.26), residues: 404 sheet: 0.16 (0.25), residues: 406 loop : -1.65 (0.17), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP N 205 HIS 0.007 0.001 HIS L 189 PHE 0.023 0.002 PHE C 724 TYR 0.022 0.002 TYR L 124 ARG 0.007 0.001 ARG C 287 Details of bonding type rmsd hydrogen bonds : bond 0.05135 ( 497) hydrogen bonds : angle 4.96572 ( 1422) covalent geometry : bond 0.00451 (15310) covalent geometry : angle 0.68103 (20829) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4869.71 seconds wall clock time: 86 minutes 49.22 seconds (5209.22 seconds total)