Starting phenix.real_space_refine on Thu Sep 18 11:00:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vml_43359/09_2025/8vml_43359_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vml_43359/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8vml_43359/09_2025/8vml_43359_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vml_43359/09_2025/8vml_43359_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vml_43359/09_2025/8vml_43359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vml_43359/09_2025/8vml_43359.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASP:plan': 9, 'GLU:plan': 16, 'GLN:plan1': 9, 'ASN:plan1': 9, 'HIS:plan': 1, '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: {'ARG:plan': 3, 'M3L:plan-1': 1, 'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2} 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: {'ARG:plan': 16, 'GLU:plan': 27, 'TYR:plan': 5, 'GLN:plan1': 10, 'PHE:plan': 6, 'ASP:plan': 15, 'ASN:plan1': 6, 'HIS:plan': 2} 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: {'GLU:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, '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: {'ASP:plan': 3, 'GLN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 1} 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: {'ARG:plan': 4, 'ASN:plan1': 2, 'GLU:plan': 5, 'ASP:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 68 Time building chain proxies: 3.68, per 1000 atoms: 0.25 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: 1.18 Conformation dependent library (CDL) restraints added in 749.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.64 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: 2.04 Time building geometry restraints manager: 1.61 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: 9.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 14.010 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.360 ------------------------------------------------------------------------------- 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 : 5.79 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.000 ARG L 439 TYR 0.010 0.001 TYR A 557 PHE 0.013 0.001 PHE A 164 TRP 0.012 0.001 TRP C 499 HIS 0.004 0.001 HIS A 527 Details of bonding type rmsd covalent geometry : bond 0.00254 (15310) covalent geometry : angle 0.61713 (20829) hydrogen bonds : bond 0.19140 ( 497) hydrogen bonds : angle 8.20646 ( 1422) *********************** 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 : 0.493 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: 0.6084 (tppt) REVERT: A 248 TYR cc_start: 0.7812 (m-80) cc_final: 0.7511 (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: 0.4203 (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: 0.6117 (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: 0.7234 (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: 0.7602 (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: 0.7486 (t0) REVERT: L 330 CYS cc_start: 0.8372 (p) cc_final: 0.8012 (m) REVERT: L 337 GLU cc_start: 0.5668 (pt0) cc_final: 0.5436 (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: 0.5283 (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: 0.6048 (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: 0.2986 (tmm-80) REVERT: P 231 LYS cc_start: 0.5224 (ttpp) cc_final: 0.4982 (ttmm) REVERT: P 253 TRP cc_start: 0.4532 (m100) cc_final: 0.4022 (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: 2 residues processed: 300 average time/residue: 0.1104 time to fit residues: 48.7513 Evaluate side-chains 216 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 214 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 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 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.0270 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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 624 HIS L 374 GLN N 27 ASN N 343 ASN P 268 HIS P 283 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.176792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.141314 restraints weight = 25005.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.143404 restraints weight = 14572.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.145188 restraints weight = 10275.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.145611 restraints weight = 8326.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.145644 restraints weight = 7529.512| |-----------------------------------------------------------------------------| r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 moved from start: 0.1811 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= 0.129 Angle : 0.616 8.876 20829 Z= 0.318 Chirality : 0.045 0.172 2327 Planarity : 0.004 0.056 2702 Dihedral : 4.338 20.472 2123 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.60 % Allowed : 16.13 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.18), residues: 1953 helix: 0.41 (0.25), residues: 428 sheet: -0.34 (0.24), residues: 403 loop : -1.58 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 439 TYR 0.017 0.001 TYR N 154 PHE 0.012 0.001 PHE N 243 TRP 0.020 0.002 TRP N 205 HIS 0.008 0.001 HIS A 481 Details of bonding type rmsd covalent geometry : bond 0.00263 (15310) covalent geometry : angle 0.61636 (20829) hydrogen bonds : bond 0.04968 ( 497) hydrogen bonds : angle 5.61530 ( 1422) *********************** 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 268 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 230 time to evaluate : 0.574 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: 0.3718 (tpt) cc_final: 0.2509 (mmt) REVERT: B 112 GLN cc_start: 0.4918 (mt0) cc_final: 0.4391 (tp40) REVERT: C 90 ASP cc_start: 0.6195 (t0) cc_final: 0.5973 (t0) REVERT: C 156 LYS cc_start: 0.5613 (ttpt) cc_final: 0.5381 (tptt) REVERT: C 504 ARG cc_start: 0.7670 (ttm-80) cc_final: 0.7084 (tpt170) REVERT: C 580 CYS cc_start: 0.7519 (m) cc_final: 0.6611 (m) REVERT: C 737 VAL cc_start: 0.6344 (t) cc_final: 0.6046 (m) REVERT: L 158 THR cc_start: 0.8879 (p) cc_final: 0.8471 (p) REVERT: N 233 VAL cc_start: 0.6643 (p) cc_final: 0.6427 (p) REVERT: N 242 LEU cc_start: 0.5681 (mm) cc_final: 0.5316 (tp) REVERT: N 287 PHE cc_start: 0.4623 (m-80) cc_final: 0.3840 (m-10) REVERT: P 216 LYS cc_start: 0.7386 (mttt) cc_final: 0.7113 (tttp) REVERT: P 231 LYS cc_start: 0.5746 (ttpp) cc_final: 0.5496 (ttmm) REVERT: P 259 ARG cc_start: 0.5796 (tpt170) cc_final: 0.4190 (mmm160) REVERT: P 286 ARG cc_start: 0.7327 (tpt-90) cc_final: 0.6804 (mtp-110) outliers start: 38 outliers final: 28 residues processed: 260 average time/residue: 0.1307 time to fit residues: 49.1894 Evaluate side-chains 216 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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 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 116 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 186 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 chunk 139 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 75 optimal weight: 20.0000 chunk 143 optimal weight: 0.9980 chunk 110 optimal weight: 0.2980 chunk 144 optimal weight: 0.9990 chunk 63 optimal weight: 20.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 527 HIS ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.174790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.139623 restraints weight = 25640.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.141496 restraints weight = 14590.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.143499 restraints weight = 10444.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.143758 restraints weight = 8375.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.143845 restraints weight = 7943.565| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15310 Z= 0.121 Angle : 0.582 7.510 20829 Z= 0.301 Chirality : 0.044 0.167 2327 Planarity : 0.004 0.051 2702 Dihedral : 4.290 21.489 2119 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.90 % Allowed : 16.06 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.18), residues: 1953 helix: 0.75 (0.25), residues: 415 sheet: -0.14 (0.24), residues: 413 loop : -1.53 (0.17), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 55 TYR 0.016 0.001 TYR A 315 PHE 0.019 0.001 PHE P 205 TRP 0.019 0.001 TRP N 205 HIS 0.007 0.001 HIS A 481 Details of bonding type rmsd covalent geometry : bond 0.00262 (15310) covalent geometry : angle 0.58205 (20829) hydrogen bonds : bond 0.04655 ( 497) hydrogen bonds : angle 5.24575 ( 1422) *********************** 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 265 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 208 time to evaluate : 0.573 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: 0.3517 (tpt) cc_final: 0.2445 (mmt) REVERT: B 112 GLN cc_start: 0.4870 (mt0) cc_final: 0.4361 (tp40) REVERT: C 90 ASP cc_start: 0.6221 (t0) cc_final: 0.6016 (t0) REVERT: C 504 ARG cc_start: 0.7748 (ttm-80) cc_final: 0.7080 (tpt170) REVERT: N 233 VAL cc_start: 0.6777 (p) cc_final: 0.6545 (p) REVERT: N 242 LEU cc_start: 0.5882 (mm) cc_final: 0.5527 (tp) REVERT: N 287 PHE cc_start: 0.4473 (m-80) cc_final: 0.3642 (m-10) REVERT: P 216 LYS cc_start: 0.7581 (mttt) cc_final: 0.7193 (tmtt) REVERT: P 253 TRP cc_start: 0.5704 (m100) cc_final: 0.5474 (m100) REVERT: P 281 ASP cc_start: 0.7872 (t0) cc_final: 0.6056 (m-30) REVERT: P 286 ARG cc_start: 0.7409 (tpt-90) cc_final: 0.6925 (mtp-110) outliers start: 57 outliers final: 40 residues processed: 247 average time/residue: 0.1283 time to fit residues: 46.6256 Evaluate side-chains 227 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 187 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 463 LEU Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 527 HIS 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 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 280 SER Chi-restraints excluded: chain C residue 448 TYR 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 246 LEU 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 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 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 129 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 118 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 169 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 161 optimal weight: 8.9990 chunk 130 optimal weight: 0.9980 chunk 166 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 chunk 150 optimal weight: 5.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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** ** C 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 191 ASN N 27 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.168367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.133643 restraints weight = 25739.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.134580 restraints weight = 15400.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.136063 restraints weight = 11860.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.136040 restraints weight = 10127.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.136425 restraints weight = 9524.662| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15310 Z= 0.166 Angle : 0.640 8.089 20829 Z= 0.334 Chirality : 0.046 0.172 2327 Planarity : 0.005 0.054 2702 Dihedral : 4.578 22.182 2119 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 4.37 % Allowed : 16.13 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.18), residues: 1953 helix: 0.84 (0.26), residues: 403 sheet: -0.10 (0.24), residues: 408 loop : -1.66 (0.17), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG N 172 TYR 0.021 0.002 TYR A 315 PHE 0.021 0.002 PHE C 724 TRP 0.019 0.002 TRP N 205 HIS 0.029 0.002 HIS A 527 Details of bonding type rmsd covalent geometry : bond 0.00380 (15310) covalent geometry : angle 0.64005 (20829) hydrogen bonds : bond 0.05147 ( 497) hydrogen bonds : angle 5.22615 ( 1422) *********************** 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 262 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 198 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.3644 (tpt) cc_final: 0.2598 (mmt) REVERT: A 300 THR cc_start: 0.5038 (t) cc_final: 0.4308 (t) REVERT: B 112 GLN cc_start: 0.4976 (mt0) cc_final: 0.4452 (tp40) REVERT: C 496 HIS cc_start: 0.7019 (OUTLIER) cc_final: 0.6756 (t-90) REVERT: C 504 ARG cc_start: 0.7850 (ttm-80) cc_final: 0.7127 (tpt170) REVERT: C 654 ARG cc_start: 0.6105 (OUTLIER) cc_final: 0.4807 (mtt90) REVERT: L 252 MET cc_start: 0.8014 (tmm) cc_final: 0.7730 (ppp) REVERT: N 242 LEU cc_start: 0.6075 (mm) cc_final: 0.5754 (tp) REVERT: N 399 MET cc_start: 0.6378 (OUTLIER) cc_final: 0.6117 (ttp) REVERT: P 216 LYS cc_start: 0.7821 (mttt) cc_final: 0.7395 (tmtt) REVERT: P 253 TRP cc_start: 0.5811 (m100) cc_final: 0.5449 (m100) REVERT: P 281 ASP cc_start: 0.7933 (t0) cc_final: 0.6165 (m-30) REVERT: P 286 ARG cc_start: 0.7465 (tpt-90) cc_final: 0.6878 (mtp85) outliers start: 64 outliers final: 47 residues processed: 245 average time/residue: 0.1288 time to fit residues: 46.6379 Evaluate side-chains 229 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 179 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 562 ASN Chi-restraints excluded: chain A residue 621 VAL 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 264 ILE Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 496 HIS Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 654 ARG Chi-restraints excluded: chain C residue 705 ASP 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 165 VAL Chi-restraints excluded: chain L residue 196 LEU Chi-restraints excluded: chain L residue 213 HIS Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 309 VAL Chi-restraints excluded: chain L residue 330 CYS Chi-restraints excluded: chain L residue 350 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 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 399 MET Chi-restraints excluded: chain N residue 404 MET Chi-restraints excluded: chain P residue 266 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 179 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 62 optimal weight: 8.9990 chunk 149 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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** L 93 ASN ** L 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.165916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.131539 restraints weight = 25980.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.132473 restraints weight = 15966.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.134202 restraints weight = 12146.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.134308 restraints weight = 9665.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.134671 restraints weight = 9220.872| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15310 Z= 0.186 Angle : 0.668 7.887 20829 Z= 0.352 Chirality : 0.046 0.189 2327 Planarity : 0.005 0.055 2702 Dihedral : 4.869 27.740 2119 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 5.13 % Allowed : 18.05 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.40 (0.18), residues: 1953 helix: 0.65 (0.25), residues: 403 sheet: -0.26 (0.24), residues: 419 loop : -1.87 (0.17), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 436 TYR 0.021 0.002 TYR A 480 PHE 0.024 0.002 PHE C 724 TRP 0.020 0.002 TRP N 49 HIS 0.036 0.002 HIS A 166 Details of bonding type rmsd covalent geometry : bond 0.00431 (15310) covalent geometry : angle 0.66804 (20829) hydrogen bonds : bond 0.05337 ( 497) hydrogen bonds : angle 5.23665 ( 1422) *********************** 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 260 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 185 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.3667 (tpt) cc_final: 0.2796 (tpp) REVERT: A 529 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7355 (tt) REVERT: B 112 GLN cc_start: 0.4891 (mt0) cc_final: 0.4316 (tp40) REVERT: C 654 ARG cc_start: 0.6154 (OUTLIER) cc_final: 0.4843 (mtt90) REVERT: L 252 MET cc_start: 0.8070 (tmm) cc_final: 0.7813 (ppp) REVERT: L 281 ASN cc_start: 0.7838 (t0) cc_final: 0.6701 (p0) REVERT: N 242 LEU cc_start: 0.6170 (mm) cc_final: 0.5927 (tp) REVERT: N 349 LYS cc_start: 0.8127 (mttt) cc_final: 0.7906 (mttp) REVERT: P 216 LYS cc_start: 0.7949 (mttt) cc_final: 0.7487 (tmtt) REVERT: P 274 LYS cc_start: 0.4448 (mmmt) cc_final: 0.4116 (mtpt) REVERT: P 281 ASP cc_start: 0.7975 (t0) cc_final: 0.6163 (m-30) REVERT: P 286 ARG cc_start: 0.7492 (tpt-90) cc_final: 0.6907 (mtp180) outliers start: 75 outliers final: 49 residues processed: 239 average time/residue: 0.1314 time to fit residues: 46.0335 Evaluate side-chains 221 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 170 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 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 562 ASN Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 53 THR 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 280 SER Chi-restraints excluded: chain C residue 448 TYR 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 165 VAL Chi-restraints excluded: chain L residue 196 LEU Chi-restraints excluded: chain L residue 213 HIS Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 309 VAL Chi-restraints excluded: chain L residue 330 CYS Chi-restraints excluded: chain L residue 350 VAL Chi-restraints excluded: chain L residue 377 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 133 MET 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 140 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 141 optimal weight: 0.6980 chunk 131 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 120 optimal weight: 0.0770 chunk 161 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 135 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 HIS A 527 HIS ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 45 ASN L 160 HIS L 235 HIS L 374 GLN L 382 GLN N 27 ASN N 397 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.168890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.134338 restraints weight = 25453.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.136361 restraints weight = 14156.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.137641 restraints weight = 10730.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.137752 restraints weight = 9005.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.138067 restraints weight = 8356.518| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15310 Z= 0.114 Angle : 0.586 8.902 20829 Z= 0.301 Chirality : 0.044 0.270 2327 Planarity : 0.004 0.047 2702 Dihedral : 4.473 23.221 2119 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.69 % Allowed : 19.55 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.18), residues: 1953 helix: 0.95 (0.26), residues: 404 sheet: -0.17 (0.25), residues: 408 loop : -1.72 (0.17), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 486 TYR 0.017 0.001 TYR A 248 PHE 0.014 0.001 PHE L 113 TRP 0.019 0.002 TRP N 205 HIS 0.020 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00246 (15310) covalent geometry : angle 0.58554 (20829) hydrogen bonds : bond 0.04380 ( 497) hydrogen bonds : angle 4.93246 ( 1422) *********************** 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 231 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 177 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ARG cc_start: 0.6098 (OUTLIER) cc_final: 0.5535 (mtm180) REVERT: A 118 MET cc_start: 0.6078 (mmt) cc_final: 0.5864 (mmt) REVERT: A 299 MET cc_start: 0.3713 (tpt) cc_final: 0.2888 (tpp) REVERT: B 112 GLN cc_start: 0.4720 (mt0) cc_final: 0.4189 (tp40) REVERT: L 220 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7810 (mt) REVERT: L 336 MET cc_start: 0.7678 (mmm) cc_final: 0.7334 (mmt) REVERT: P 216 LYS cc_start: 0.7947 (mttt) cc_final: 0.7413 (tmtt) REVERT: P 274 LYS cc_start: 0.4270 (mmmt) cc_final: 0.3958 (mtpt) REVERT: P 281 ASP cc_start: 0.7873 (t0) cc_final: 0.6068 (m-30) REVERT: P 286 ARG cc_start: 0.7567 (tpt-90) cc_final: 0.6893 (mtp85) outliers start: 54 outliers final: 39 residues processed: 220 average time/residue: 0.1209 time to fit residues: 39.6219 Evaluate side-chains 206 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 165 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 113 ARG 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 527 HIS 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 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 530 CYS Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 734 LEU Chi-restraints excluded: chain C residue 742 GLU Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 213 HIS Chi-restraints excluded: chain L residue 220 ILE 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 133 MET 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 278 CYS Chi-restraints excluded: chain N residue 287 PHE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 174 optimal weight: 0.3980 chunk 191 optimal weight: 7.9990 chunk 173 optimal weight: 0.9990 chunk 109 optimal weight: 0.0870 chunk 38 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 overall best weight: 1.8964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 527 HIS ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 45 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 = 0.4244 r_free = 0.4244 target = 0.164861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.130202 restraints weight = 25997.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.132112 restraints weight = 14894.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.133563 restraints weight = 11151.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.133597 restraints weight = 9567.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.133704 restraints weight = 8981.471| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15310 Z= 0.184 Angle : 0.662 8.839 20829 Z= 0.346 Chirality : 0.046 0.218 2327 Planarity : 0.005 0.053 2702 Dihedral : 4.776 24.854 2119 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 4.58 % Allowed : 19.69 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.18), residues: 1953 helix: 0.78 (0.26), residues: 405 sheet: -0.16 (0.25), residues: 408 loop : -1.90 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 46 TYR 0.018 0.002 TYR L 124 PHE 0.023 0.002 PHE A 165 TRP 0.018 0.002 TRP N 205 HIS 0.020 0.002 HIS A 527 Details of bonding type rmsd covalent geometry : bond 0.00426 (15310) covalent geometry : angle 0.66215 (20829) hydrogen bonds : bond 0.05183 ( 497) hydrogen bonds : angle 5.10328 ( 1422) *********************** 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 243 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 176 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 ARG cc_start: 0.6313 (OUTLIER) cc_final: 0.5679 (mtm180) REVERT: A 299 MET cc_start: 0.3398 (tpt) cc_final: 0.2747 (tpp) REVERT: B 112 GLN cc_start: 0.4850 (mt0) cc_final: 0.4253 (tp40) REVERT: C 654 ARG cc_start: 0.6221 (OUTLIER) cc_final: 0.4903 (mtt90) REVERT: L 281 ASN cc_start: 0.7890 (t0) cc_final: 0.6833 (p0) REVERT: P 216 LYS cc_start: 0.8005 (mttt) cc_final: 0.7530 (tmtt) REVERT: P 259 ARG cc_start: 0.5866 (tpt170) cc_final: 0.5023 (tpp-160) REVERT: P 281 ASP cc_start: 0.7954 (t0) cc_final: 0.6168 (m-30) REVERT: P 286 ARG cc_start: 0.7529 (tpt-90) cc_final: 0.6860 (mtp85) outliers start: 67 outliers final: 49 residues processed: 228 average time/residue: 0.1266 time to fit residues: 42.3604 Evaluate side-chains 222 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 171 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 113 ARG Chi-restraints excluded: chain A residue 161 PHE Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 636 CYS 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 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 C residue 737 VAL Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 183 ILE 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 391 LEU Chi-restraints excluded: chain L residue 424 ILE Chi-restraints excluded: chain N residue 31 LEU 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 133 MET 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 390 ILE Chi-restraints excluded: chain N residue 391 CYS Chi-restraints excluded: chain P residue 211 ILE 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 185 optimal weight: 1.9990 chunk 187 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 151 optimal weight: 7.9990 chunk 177 optimal weight: 0.9980 chunk 172 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 74 optimal weight: 0.0870 chunk 108 optimal weight: 10.0000 overall best weight: 0.7360 ------------------------------------------------------------------------------- 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 507 HIS A 527 HIS ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 45 ASN ** L 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 266 ASN N 27 ASN N 397 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.168271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.135264 restraints weight = 25716.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.136825 restraints weight = 14503.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.138175 restraints weight = 10891.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.138658 restraints weight = 8968.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.138696 restraints weight = 8390.280| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15310 Z= 0.116 Angle : 0.592 7.664 20829 Z= 0.306 Chirality : 0.044 0.189 2327 Planarity : 0.004 0.061 2702 Dihedral : 4.452 23.186 2119 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.62 % Allowed : 21.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.18), residues: 1953 helix: 1.03 (0.26), residues: 403 sheet: -0.07 (0.25), residues: 410 loop : -1.79 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 486 TYR 0.017 0.001 TYR N 21 PHE 0.013 0.001 PHE L 113 TRP 0.018 0.001 TRP N 205 HIS 0.023 0.001 HIS A 527 Details of bonding type rmsd covalent geometry : bond 0.00252 (15310) covalent geometry : angle 0.59189 (20829) hydrogen bonds : bond 0.04309 ( 497) hydrogen bonds : angle 4.86176 ( 1422) *********************** 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 236 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 183 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.6675 (mmt) cc_final: 0.5746 (mmt) REVERT: A 299 MET cc_start: 0.3646 (tpt) cc_final: 0.2928 (tpp) REVERT: A 319 MET cc_start: 0.4258 (mmm) cc_final: 0.3813 (mmm) REVERT: B 112 GLN cc_start: 0.4798 (mt0) cc_final: 0.4212 (tp40) REVERT: L 281 ASN cc_start: 0.7817 (t0) cc_final: 0.6784 (p0) REVERT: N 143 LYS cc_start: 0.4127 (mmtt) cc_final: 0.2340 (mtpt) REVERT: P 216 LYS cc_start: 0.7911 (mttt) cc_final: 0.7505 (tmtt) REVERT: P 259 ARG cc_start: 0.5840 (tpt170) cc_final: 0.5015 (tpp-160) REVERT: P 281 ASP cc_start: 0.7854 (t0) cc_final: 0.6059 (m-30) REVERT: P 286 ARG cc_start: 0.7512 (tpt-90) cc_final: 0.6880 (mtp85) outliers start: 53 outliers final: 47 residues processed: 226 average time/residue: 0.1165 time to fit residues: 39.9405 Evaluate side-chains 219 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 172 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 113 ARG 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 527 HIS Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 636 CYS 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 530 CYS Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 734 LEU Chi-restraints excluded: chain L residue 115 THR 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 266 ASN 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 L residue 428 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 133 MET 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 287 PHE Chi-restraints excluded: chain N residue 303 LEU 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 91 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 31 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 chunk 66 optimal weight: 0.0050 chunk 129 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 507 HIS A 527 HIS ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 266 ASN N 27 ASN N 123 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.168282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.135063 restraints weight = 25746.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.137114 restraints weight = 14704.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.138321 restraints weight = 11033.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.138281 restraints weight = 9280.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.138476 restraints weight = 8615.445| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.4444 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= 0.117 Angle : 0.590 8.225 20829 Z= 0.304 Chirality : 0.044 0.177 2327 Planarity : 0.004 0.055 2702 Dihedral : 4.363 23.511 2119 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 3.83 % Allowed : 21.05 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.19), residues: 1953 helix: 1.12 (0.26), residues: 403 sheet: -0.01 (0.25), residues: 410 loop : -1.72 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 185 TYR 0.014 0.001 TYR C 574 PHE 0.028 0.001 PHE A 165 TRP 0.018 0.001 TRP N 205 HIS 0.012 0.001 HIS A 527 Details of bonding type rmsd covalent geometry : bond 0.00254 (15310) covalent geometry : angle 0.58984 (20829) hydrogen bonds : bond 0.04204 ( 497) hydrogen bonds : angle 4.78363 ( 1422) *********************** 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 231 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 175 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.6751 (mmt) cc_final: 0.5812 (mmt) REVERT: A 299 MET cc_start: 0.3820 (tpt) cc_final: 0.3022 (tpp) REVERT: B 112 GLN cc_start: 0.4789 (mt0) cc_final: 0.4202 (tp40) REVERT: C 636 GLU cc_start: 0.6082 (mm-30) cc_final: 0.5853 (mm-30) REVERT: C 654 ARG cc_start: 0.6097 (OUTLIER) cc_final: 0.4748 (mtt90) REVERT: L 281 ASN cc_start: 0.7800 (t0) cc_final: 0.6784 (p0) REVERT: N 143 LYS cc_start: 0.4079 (mmtt) cc_final: 0.2328 (mtpt) REVERT: P 216 LYS cc_start: 0.7896 (mttt) cc_final: 0.7486 (tmtt) REVERT: P 259 ARG cc_start: 0.5923 (tpt170) cc_final: 0.5086 (tpp-160) REVERT: P 281 ASP cc_start: 0.7792 (t0) cc_final: 0.5979 (m-30) REVERT: P 286 ARG cc_start: 0.7551 (tpt-90) cc_final: 0.6865 (mtp85) outliers start: 56 outliers final: 50 residues processed: 222 average time/residue: 0.1156 time to fit residues: 38.3033 Evaluate side-chains 223 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 172 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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 113 ARG Chi-restraints excluded: chain A residue 161 PHE Chi-restraints excluded: chain A residue 237 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 A residue 636 CYS 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 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 C residue 737 VAL Chi-restraints excluded: chain L residue 115 THR 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 266 ASN 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 L residue 428 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 133 MET 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 287 PHE Chi-restraints excluded: chain N residue 303 LEU Chi-restraints excluded: chain N residue 348 SER Chi-restraints excluded: chain N residue 385 ASN Chi-restraints excluded: chain N residue 391 CYS Chi-restraints excluded: chain P residue 204 CYS Chi-restraints excluded: chain P residue 211 ILE 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 187 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 90 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 HIS A 507 HIS ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 266 ASN L 374 GLN N 27 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.166183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.133703 restraints weight = 26088.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.134189 restraints weight = 15292.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.136610 restraints weight = 11426.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.136436 restraints weight = 8954.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.136962 restraints weight = 9066.086| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15310 Z= 0.157 Angle : 0.633 7.975 20829 Z= 0.328 Chirality : 0.045 0.177 2327 Planarity : 0.005 0.054 2702 Dihedral : 4.532 24.893 2119 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 3.83 % Allowed : 20.78 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.18), residues: 1953 helix: 1.00 (0.26), residues: 404 sheet: -0.07 (0.26), residues: 402 loop : -1.82 (0.17), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 486 TYR 0.014 0.002 TYR L 124 PHE 0.019 0.002 PHE C 724 TRP 0.018 0.002 TRP N 205 HIS 0.012 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00364 (15310) covalent geometry : angle 0.63293 (20829) hydrogen bonds : bond 0.04687 ( 497) hydrogen bonds : angle 4.88218 ( 1422) ********************** 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 230 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 174 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 ARG cc_start: 0.6317 (OUTLIER) cc_final: 0.5759 (mtm180) REVERT: A 118 MET cc_start: 0.6797 (mmt) cc_final: 0.5838 (mmt) REVERT: A 299 MET cc_start: 0.3963 (tpt) cc_final: 0.3160 (tpp) REVERT: A 319 MET cc_start: 0.3989 (mmm) cc_final: 0.2430 (mmm) REVERT: C 654 ARG cc_start: 0.6163 (OUTLIER) cc_final: 0.4999 (mtt90) REVERT: L 281 ASN cc_start: 0.7808 (t0) cc_final: 0.6758 (p0) REVERT: N 143 LYS cc_start: 0.4132 (mmtt) cc_final: 0.2380 (mtpt) REVERT: P 216 LYS cc_start: 0.7974 (mttt) cc_final: 0.7432 (tptm) REVERT: P 259 ARG cc_start: 0.5983 (tpt170) cc_final: 0.5173 (tpp-160) REVERT: P 281 ASP cc_start: 0.7838 (t0) cc_final: 0.6040 (m-30) REVERT: P 286 ARG cc_start: 0.7533 (tpt-90) cc_final: 0.6930 (mtp180) outliers start: 56 outliers final: 50 residues processed: 220 average time/residue: 0.1229 time to fit residues: 40.7127 Evaluate side-chains 222 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 170 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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 113 ARG Chi-restraints excluded: chain A residue 166 HIS Chi-restraints excluded: chain A residue 237 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 592 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 636 CYS 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 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 C residue 737 VAL Chi-restraints excluded: chain L residue 115 THR 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 266 ASN 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 391 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 53 VAL Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 133 MET 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 287 PHE Chi-restraints excluded: chain N residue 303 LEU Chi-restraints excluded: chain N residue 348 SER Chi-restraints excluded: chain N residue 385 ASN Chi-restraints excluded: chain N residue 391 CYS Chi-restraints excluded: chain P residue 190 PHE Chi-restraints excluded: chain P residue 204 CYS Chi-restraints excluded: chain P residue 211 ILE 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 130 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 chunk 173 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 190 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 33 optimal weight: 0.0470 chunk 115 optimal weight: 0.7980 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 HIS A 527 HIS ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 266 ASN L 374 GLN N 27 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.166783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.133227 restraints weight = 25783.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.134739 restraints weight = 15798.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.136790 restraints weight = 11299.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.136768 restraints weight = 8878.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.137037 restraints weight = 8918.551| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15310 Z= 0.136 Angle : 0.615 7.868 20829 Z= 0.317 Chirality : 0.045 0.171 2327 Planarity : 0.004 0.053 2702 Dihedral : 4.490 23.813 2119 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 3.96 % Allowed : 21.05 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.18), residues: 1953 helix: 1.06 (0.26), residues: 404 sheet: -0.09 (0.26), residues: 404 loop : -1.81 (0.17), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 486 TYR 0.017 0.001 TYR N 21 PHE 0.027 0.002 PHE A 164 TRP 0.018 0.002 TRP N 205 HIS 0.005 0.001 HIS N 226 Details of bonding type rmsd covalent geometry : bond 0.00308 (15310) covalent geometry : angle 0.61465 (20829) hydrogen bonds : bond 0.04448 ( 497) hydrogen bonds : angle 4.84819 ( 1422) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2659.36 seconds wall clock time: 46 minutes 55.94 seconds (2815.94 seconds total)