Starting phenix.real_space_refine on Sat Jun 14 13:52:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vml_43359/06_2025/8vml_43359_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vml_43359/06_2025/8vml_43359.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vml_43359/06_2025/8vml_43359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vml_43359/06_2025/8vml_43359.map" model { file = "/net/cci-nas-00/data/ceres_data/8vml_43359/06_2025/8vml_43359_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vml_43359/06_2025/8vml_43359_neut.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1328 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 94 5.16 5 C 9472 2.51 5 N 2687 2.21 5 O 2694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14947 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3340 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 19, 'TRANS': 419} Chain breaks: 7 Unresolved non-hydrogen bonds: 294 Unresolved non-hydrogen angles: 356 Unresolved non-hydrogen dihedrals: 234 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 9, 'ASN:plan1': 9, 'HIS:plan': 1, 'GLU:plan': 16, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 184 Chain: "B" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 290 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 36} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'M3L:plan-1': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 4278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4278 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PTRANS': 33, 'TRANS': 572} Chain breaks: 2 Unresolved non-hydrogen bonds: 604 Unresolved non-hydrogen angles: 753 Unresolved non-hydrogen dihedrals: 486 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 6, 'ASP:plan': 15, 'PHE:plan': 6, 'GLU:plan': 27, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 372 Chain: "I" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 156 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 19} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 2874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2874 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 12, 'TRANS': 349} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "N" Number of atoms: 3080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3080 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 22, 'TRANS': 372} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 42 Chain: "P" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 929 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 7, 'TRANS': 118} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Time building chain proxies: 10.23, per 1000 atoms: 0.68 Number of scatterers: 14947 At special positions: 0 Unit cell: (159.96, 116.96, 101.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 94 16.00 O 2694 8.00 N 2687 7.00 C 9472 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.37 Conformation dependent library (CDL) restraints added in 1.8 seconds 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3808 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 24 sheets defined 25.3% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 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: 5.21 Time building geometry restraints manager: 3.90 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: 0.010 Normalize map: mean=0, sd=1: 6.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 36.830 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5807 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15310 Z= 0.130 Angle : 0.617 8.713 20829 Z= 0.351 Chirality : 0.041 0.151 2327 Planarity : 0.004 0.048 2702 Dihedral : 14.245 88.812 5324 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.55 % Allowed : 14.70 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.18), residues: 1953 helix: -0.09 (0.26), residues: 408 sheet: -0.61 (0.25), residues: 401 loop : -1.61 (0.17), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 499 HIS 0.004 0.001 HIS A 527 PHE 0.013 0.001 PHE A 164 TYR 0.010 0.001 TYR A 557 ARG 0.006 0.000 ARG L 439 Details of bonding type rmsd hydrogen bonds : bond 0.19140 ( 497) hydrogen bonds : angle 8.20646 ( 1422) covalent geometry : bond 0.00254 (15310) covalent geometry : angle 0.61713 (20829) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 298 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 LYS cc_start: 0.6428 (tttt) cc_final: 0.6083 (tppt) REVERT: A 248 TYR cc_start: 0.7812 (m-80) cc_final: 0.7510 (m-80) REVERT: A 495 TYR cc_start: 0.6564 (t80) cc_final: 0.6295 (t80) REVERT: B 112 GLN cc_start: 0.4793 (mt0) cc_final: 0.4202 (tp40) REVERT: C 90 ASP cc_start: 0.7009 (t0) cc_final: 0.6749 (t0) REVERT: C 156 LYS cc_start: 0.4795 (ttpt) cc_final: 0.4581 (tptt) REVERT: C 264 ILE cc_start: 0.6783 (tt) cc_final: 0.6118 (mm) REVERT: C 290 PHE cc_start: 0.6424 (m-80) cc_final: 0.6092 (m-80) REVERT: C 504 ARG cc_start: 0.7877 (ttm-80) cc_final: 0.7235 (tpt170) REVERT: C 580 CYS cc_start: 0.8099 (m) cc_final: 0.7228 (m) REVERT: L 158 THR cc_start: 0.8083 (p) cc_final: 0.7601 (p) REVERT: L 160 HIS cc_start: 0.7976 (m170) cc_final: 0.7608 (m170) REVERT: L 243 ASP cc_start: 0.7795 (t0) cc_final: 0.7484 (t0) REVERT: L 330 CYS cc_start: 0.8372 (p) cc_final: 0.8011 (m) REVERT: L 337 GLU cc_start: 0.5668 (pt0) cc_final: 0.5431 (tm-30) REVERT: L 376 MET cc_start: 0.6803 (ttp) cc_final: 0.6538 (ttm) REVERT: L 389 TRP cc_start: 0.5721 (m-90) cc_final: 0.5282 (m100) REVERT: N 36 MET cc_start: 0.4744 (mmm) cc_final: 0.4453 (ttm) REVERT: N 233 VAL cc_start: 0.6340 (p) cc_final: 0.6049 (p) REVERT: N 376 LYS cc_start: 0.7098 (tttt) cc_final: 0.6830 (tttp) REVERT: P 216 LYS cc_start: 0.6827 (mttt) cc_final: 0.6247 (tttp) REVERT: P 230 ARG cc_start: 0.3267 (ptt180) cc_final: 0.2985 (tmm-80) REVERT: P 231 LYS cc_start: 0.5224 (ttpp) cc_final: 0.4981 (ttmm) REVERT: P 253 TRP cc_start: 0.4532 (m100) cc_final: 0.4021 (m100) REVERT: P 281 ASP cc_start: 0.7354 (t0) cc_final: 0.6114 (m-30) REVERT: P 286 ARG cc_start: 0.7029 (tpt-90) cc_final: 0.5878 (mtp-110) outliers start: 8 outliers final: 3 residues processed: 300 average time/residue: 0.3052 time to fit residues: 134.4101 Evaluate side-chains 217 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 214 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain L residue 349 ASN Chi-restraints excluded: chain L residue 363 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 6.9990 chunk 148 optimal weight: 0.6980 chunk 82 optimal weight: 7.9990 chunk 50 optimal weight: 0.6980 chunk 100 optimal weight: 0.4980 chunk 79 optimal weight: 9.9990 chunk 153 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 177 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 241 ASN A 527 HIS A 624 HIS C 502 HIS L 374 GLN N 27 ASN P 268 HIS P 283 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.176843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.140616 restraints weight = 25116.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.144306 restraints weight = 14489.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.145167 restraints weight = 9888.893| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15310 Z= 0.128 Angle : 0.616 9.431 20829 Z= 0.318 Chirality : 0.045 0.171 2327 Planarity : 0.004 0.057 2702 Dihedral : 4.358 23.382 2125 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.67 % Allowed : 15.99 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.18), residues: 1953 helix: 0.44 (0.25), residues: 423 sheet: -0.34 (0.24), residues: 403 loop : -1.56 (0.17), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP N 205 HIS 0.006 0.001 HIS A 481 PHE 0.012 0.001 PHE C 285 TYR 0.016 0.001 TYR N 154 ARG 0.006 0.001 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.05053 ( 497) hydrogen bonds : angle 5.64342 ( 1422) covalent geometry : bond 0.00264 (15310) covalent geometry : angle 0.61578 (20829) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 235 time to evaluate : 1.749 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: 0.3706 (tpt) cc_final: 0.2375 (mmt) REVERT: B 112 GLN cc_start: 0.4951 (mt0) cc_final: 0.4416 (tp40) REVERT: C 90 ASP cc_start: 0.6216 (t0) cc_final: 0.6005 (t0) REVERT: C 156 LYS cc_start: 0.5585 (ttpt) cc_final: 0.5362 (tptt) REVERT: C 504 ARG cc_start: 0.7723 (ttm-80) cc_final: 0.7085 (tpt170) REVERT: C 580 CYS cc_start: 0.7539 (m) cc_final: 0.6645 (m) REVERT: C 737 VAL cc_start: 0.6310 (t) cc_final: 0.6010 (m) REVERT: L 158 THR cc_start: 0.8869 (p) cc_final: 0.8457 (p) REVERT: N 233 VAL cc_start: 0.6634 (p) cc_final: 0.6419 (p) REVERT: N 242 LEU cc_start: 0.5787 (mm) cc_final: 0.5413 (tp) REVERT: N 287 PHE cc_start: 0.4574 (m-80) cc_final: 0.3790 (m-10) REVERT: N 402 TRP cc_start: 0.7232 (p-90) cc_final: 0.7031 (p-90) REVERT: P 216 LYS cc_start: 0.7374 (mttt) cc_final: 0.7111 (tttp) REVERT: P 230 ARG cc_start: 0.3539 (ptt180) cc_final: 0.3114 (tmm-80) REVERT: P 231 LYS cc_start: 0.5739 (ttpp) cc_final: 0.5500 (ttmm) REVERT: P 253 TRP cc_start: 0.5508 (m100) cc_final: 0.4422 (m100) REVERT: P 286 ARG cc_start: 0.7346 (tpt-90) cc_final: 0.6799 (mtp-110) outliers start: 39 outliers final: 29 residues processed: 264 average time/residue: 0.2825 time to fit residues: 108.2276 Evaluate side-chains 222 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 193 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 HIS Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 705 ASP Chi-restraints excluded: chain L residue 128 SER Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 196 LEU Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 405 THR Chi-restraints excluded: chain L residue 424 ILE Chi-restraints excluded: chain L residue 425 LEU Chi-restraints excluded: chain N residue 234 SER Chi-restraints excluded: chain N residue 257 THR Chi-restraints excluded: chain N residue 267 HIS Chi-restraints excluded: chain N residue 348 SER Chi-restraints excluded: chain N residue 391 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 177 optimal weight: 0.5980 chunk 159 optimal weight: 0.0770 chunk 185 optimal weight: 0.0370 chunk 143 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 138 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 182 optimal weight: 0.0470 overall best weight: 0.3114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 548 GLN L 160 HIS N 27 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.177493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.141787 restraints weight = 25126.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.143729 restraints weight = 14633.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.145576 restraints weight = 10349.331| |-----------------------------------------------------------------------------| r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 moved from start: 0.2276 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= 0.106 Angle : 0.560 7.597 20829 Z= 0.288 Chirality : 0.043 0.165 2327 Planarity : 0.004 0.050 2702 Dihedral : 4.202 21.219 2119 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.28 % Allowed : 16.75 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.18), residues: 1953 helix: 0.76 (0.25), residues: 417 sheet: -0.22 (0.24), residues: 422 loop : -1.42 (0.18), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP N 205 HIS 0.012 0.001 HIS A 527 PHE 0.027 0.001 PHE C 469 TYR 0.015 0.001 TYR A 495 ARG 0.007 0.000 ARG N 55 Details of bonding type rmsd hydrogen bonds : bond 0.04382 ( 497) hydrogen bonds : angle 5.18173 ( 1422) covalent geometry : bond 0.00217 (15310) covalent geometry : angle 0.55968 (20829) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 208 time to evaluate : 1.673 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: 0.3550 (tpt) cc_final: 0.2436 (mmt) REVERT: A 311 LEU cc_start: 0.5776 (OUTLIER) cc_final: 0.5555 (pp) REVERT: B 112 GLN cc_start: 0.4851 (mt0) cc_final: 0.4351 (tp40) REVERT: B 143 GLN cc_start: 0.6363 (OUTLIER) cc_final: 0.6069 (mp10) REVERT: C 90 ASP cc_start: 0.6282 (t0) cc_final: 0.6073 (t0) REVERT: C 156 LYS cc_start: 0.5451 (ttpt) cc_final: 0.5248 (tptt) REVERT: C 508 LEU cc_start: 0.6868 (OUTLIER) cc_final: 0.6575 (mt) REVERT: L 133 ARG cc_start: 0.7070 (ttp80) cc_final: 0.6858 (tpt90) REVERT: L 376 MET cc_start: 0.6670 (mtp) cc_final: 0.6317 (ttm) REVERT: N 233 VAL cc_start: 0.6701 (p) cc_final: 0.6443 (p) REVERT: N 242 LEU cc_start: 0.5882 (mm) cc_final: 0.5506 (tp) REVERT: N 287 PHE cc_start: 0.4346 (m-80) cc_final: 0.3628 (m-10) REVERT: P 216 LYS cc_start: 0.7441 (mttt) cc_final: 0.7112 (tttp) REVERT: P 253 TRP cc_start: 0.5650 (m100) cc_final: 0.4535 (m100) REVERT: P 281 ASP cc_start: 0.7741 (t0) cc_final: 0.5785 (m-30) REVERT: P 286 ARG cc_start: 0.7379 (tpt-90) cc_final: 0.6939 (mtp-110) outliers start: 48 outliers final: 31 residues processed: 243 average time/residue: 0.2873 time to fit residues: 102.2613 Evaluate side-chains 223 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 189 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 HIS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 330 CYS Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 424 ILE Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 144 THR Chi-restraints excluded: chain N residue 224 THR Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 257 THR Chi-restraints excluded: chain N residue 267 HIS Chi-restraints excluded: chain N residue 348 SER Chi-restraints excluded: chain N residue 391 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 50 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 157 optimal weight: 7.9990 chunk 165 optimal weight: 0.2980 chunk 46 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 192 optimal weight: 10.0000 chunk 169 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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** L 160 HIS L 191 ASN N 27 ASN N 343 ASN ** N 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.169514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.134028 restraints weight = 25640.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.136131 restraints weight = 15365.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.137713 restraints weight = 10923.031| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15310 Z= 0.161 Angle : 0.631 7.694 20829 Z= 0.330 Chirality : 0.046 0.175 2327 Planarity : 0.005 0.053 2702 Dihedral : 4.534 21.600 2119 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 4.44 % Allowed : 16.13 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.18), residues: 1953 helix: 0.88 (0.26), residues: 408 sheet: -0.08 (0.24), residues: 415 loop : -1.59 (0.17), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP N 205 HIS 0.027 0.001 HIS A 83 PHE 0.021 0.002 PHE C 724 TYR 0.018 0.002 TYR N 154 ARG 0.005 0.001 ARG N 172 Details of bonding type rmsd hydrogen bonds : bond 0.05116 ( 497) hydrogen bonds : angle 5.22006 ( 1422) covalent geometry : bond 0.00365 (15310) covalent geometry : angle 0.63116 (20829) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 203 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.3627 (tpt) cc_final: 0.2771 (tpp) REVERT: A 302 PHE cc_start: 0.7268 (m-80) cc_final: 0.7041 (m-10) REVERT: A 529 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.7139 (tt) REVERT: B 112 GLN cc_start: 0.4888 (mt0) cc_final: 0.4367 (tp40) REVERT: B 143 GLN cc_start: 0.6637 (OUTLIER) cc_final: 0.6339 (mp10) REVERT: C 496 HIS cc_start: 0.6971 (OUTLIER) cc_final: 0.6551 (t-90) REVERT: C 508 LEU cc_start: 0.6765 (OUTLIER) cc_final: 0.6411 (mt) REVERT: N 194 LEU cc_start: 0.6421 (mt) cc_final: 0.6187 (mt) REVERT: N 242 LEU cc_start: 0.6155 (mm) cc_final: 0.5815 (tp) REVERT: P 216 LYS cc_start: 0.7798 (mttt) cc_final: 0.7387 (tmtt) REVERT: P 253 TRP cc_start: 0.5765 (m100) cc_final: 0.4943 (m100) REVERT: P 259 ARG cc_start: 0.5418 (tpt170) cc_final: 0.4220 (tpp-160) REVERT: P 281 ASP cc_start: 0.7895 (t0) cc_final: 0.6156 (m-30) REVERT: P 286 ARG cc_start: 0.7477 (tpt-90) cc_final: 0.6914 (mtp85) outliers start: 65 outliers final: 43 residues processed: 252 average time/residue: 0.2595 time to fit residues: 97.5781 Evaluate side-chains 232 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 185 time to evaluate : 1.594 ------------------------------------------------------------------------------- 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 506 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 496 HIS Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 734 LEU Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 128 SER Chi-restraints excluded: chain L residue 160 HIS Chi-restraints excluded: chain L residue 196 LEU Chi-restraints excluded: chain L residue 213 HIS Chi-restraints excluded: chain L residue 309 VAL Chi-restraints excluded: chain L residue 330 CYS Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 405 THR Chi-restraints excluded: chain L residue 424 ILE Chi-restraints excluded: chain N residue 27 ASN 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 273 THR Chi-restraints excluded: chain N residue 278 CYS Chi-restraints excluded: chain N residue 303 LEU Chi-restraints excluded: chain N residue 348 SER Chi-restraints excluded: chain N residue 391 CYS Chi-restraints excluded: chain N residue 404 MET Chi-restraints excluded: chain P residue 266 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 124 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 chunk 11 optimal weight: 40.0000 chunk 15 optimal weight: 20.0000 chunk 102 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 374 GLN L 382 GLN N 27 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.169533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.134295 restraints weight = 25920.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.136349 restraints weight = 15333.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.137675 restraints weight = 11353.145| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.3345 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= 0.129 Angle : 0.583 7.660 20829 Z= 0.304 Chirality : 0.044 0.160 2327 Planarity : 0.004 0.048 2702 Dihedral : 4.422 22.520 2119 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.51 % Allowed : 16.75 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.18), residues: 1953 helix: 1.05 (0.26), residues: 403 sheet: 0.04 (0.25), residues: 403 loop : -1.61 (0.17), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP N 205 HIS 0.013 0.001 HIS A 166 PHE 0.015 0.001 PHE C 724 TYR 0.022 0.001 TYR A 480 ARG 0.005 0.000 ARG C 504 Details of bonding type rmsd hydrogen bonds : bond 0.04545 ( 497) hydrogen bonds : angle 5.01469 ( 1422) covalent geometry : bond 0.00285 (15310) covalent geometry : angle 0.58304 (20829) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 195 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 HIS cc_start: 0.8436 (t-90) cc_final: 0.8053 (m-70) REVERT: A 299 MET cc_start: 0.3692 (tpt) cc_final: 0.3018 (tpp) REVERT: A 300 THR cc_start: 0.4901 (t) cc_final: 0.4356 (t) REVERT: A 529 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6987 (tt) REVERT: B 112 GLN cc_start: 0.4991 (mt0) cc_final: 0.4421 (tp40) REVERT: C 439 MET cc_start: 0.6447 (tpp) cc_final: 0.6236 (tpp) REVERT: C 496 HIS cc_start: 0.7094 (OUTLIER) cc_final: 0.6807 (t-90) REVERT: C 508 LEU cc_start: 0.6813 (OUTLIER) cc_final: 0.6466 (mt) REVERT: C 654 ARG cc_start: 0.6063 (OUTLIER) cc_final: 0.4757 (mtt90) REVERT: N 242 LEU cc_start: 0.6163 (mm) cc_final: 0.5936 (tp) REVERT: P 216 LYS cc_start: 0.7831 (mttt) cc_final: 0.7430 (tmtt) REVERT: P 230 ARG cc_start: 0.2157 (OUTLIER) cc_final: 0.1700 (ttm170) REVERT: P 259 ARG cc_start: 0.5387 (tpt170) cc_final: 0.4189 (tpp-160) REVERT: P 274 LYS cc_start: 0.4457 (mmmt) cc_final: 0.4071 (mtpt) REVERT: P 281 ASP cc_start: 0.7796 (t0) cc_final: 0.6000 (m-30) REVERT: P 286 ARG cc_start: 0.7490 (tpt-90) cc_final: 0.6844 (mtp85) outliers start: 66 outliers final: 44 residues processed: 248 average time/residue: 0.2856 time to fit residues: 103.9503 Evaluate side-chains 232 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 183 time to evaluate : 1.746 ------------------------------------------------------------------------------- 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 592 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 129 HIS Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 496 HIS Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 654 ARG Chi-restraints excluded: chain C residue 734 LEU Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 128 SER Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 213 HIS Chi-restraints excluded: chain L residue 309 VAL Chi-restraints excluded: chain L residue 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 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 287 PHE Chi-restraints excluded: chain N residue 348 SER Chi-restraints excluded: chain N residue 391 CYS Chi-restraints excluded: chain N residue 404 MET Chi-restraints excluded: chain P residue 230 ARG Chi-restraints excluded: chain P residue 266 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.1576 > 50: distance: 35 - 94: 33.698 distance: 38 - 91: 36.401 distance: 49 - 78: 32.516 distance: 52 - 75: 35.531 distance: 66 - 69: 34.543 distance: 69 - 70: 40.752 distance: 69 - 168: 33.087 distance: 70 - 71: 41.410 distance: 73 - 74: 69.527 distance: 75 - 76: 39.593 distance: 76 - 79: 57.609 distance: 77 - 78: 57.209 distance: 77 - 82: 69.864 distance: 79 - 80: 38.997 distance: 79 - 81: 39.342 distance: 82 - 83: 60.802 distance: 83 - 84: 47.352 distance: 83 - 86: 22.182 distance: 84 - 85: 40.697 distance: 88 - 89: 40.047 distance: 91 - 92: 39.642 distance: 92 - 93: 41.408 distance: 92 - 95: 55.186 distance: 93 - 99: 40.252 distance: 95 - 96: 55.169 distance: 96 - 97: 57.564 distance: 96 - 98: 19.791 distance: 99 - 100: 55.636 distance: 99 - 105: 40.089 distance: 100 - 101: 56.145 distance: 100 - 103: 57.418 distance: 101 - 102: 40.211 distance: 103 - 104: 56.218 distance: 104 - 105: 40.441 distance: 106 - 107: 68.761 distance: 107 - 108: 40.051 distance: 107 - 110: 40.071 distance: 108 - 109: 57.411 distance: 108 - 114: 39.001 distance: 110 - 111: 56.486 distance: 111 - 113: 9.268 distance: 114 - 115: 56.693 distance: 115 - 116: 38.644 distance: 115 - 118: 34.651 distance: 116 - 117: 40.832 distance: 116 - 122: 40.065 distance: 118 - 119: 6.385 distance: 119 - 120: 41.199 distance: 119 - 121: 45.534 distance: 122 - 123: 38.938 distance: 123 - 124: 56.325 distance: 123 - 126: 39.876 distance: 124 - 125: 57.550 distance: 124 - 127: 39.190 distance: 127 - 128: 39.801 distance: 128 - 131: 39.170 distance: 129 - 130: 56.343 distance: 132 - 133: 55.637 distance: 133 - 134: 56.936 distance: 133 - 136: 57.829 distance: 134 - 135: 70.047 distance: 134 - 137: 34.142