Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 23:09:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mts_23996/04_2023/7mts_23996_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mts_23996/04_2023/7mts_23996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mts_23996/04_2023/7mts_23996.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mts_23996/04_2023/7mts_23996.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mts_23996/04_2023/7mts_23996_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mts_23996/04_2023/7mts_23996_updated.pdb" } resolution = 3.2 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 ------------------------------------------------------------------------------- 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= 0.004 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 109 5.16 5 C 10258 2.51 5 N 2787 2.21 5 O 2914 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 225": "OE1" <-> "OE2" Residue "C GLU 25": "OE1" <-> "OE2" Residue "C GLU 318": "OE1" <-> "OE2" Residue "E GLU 22": "OE1" <-> "OE2" Residue "A GLU 902": "OE1" <-> "OE2" Residue "B GLU 901": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 16068 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 6003 Classifications: {'peptide': 783} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 38, 'TRANS': 744} Chain breaks: 2 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 8, 'ARG:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 79 Chain: "B" Number of atoms: 5773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 763, 5773 Classifications: {'peptide': 763} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 37, 'TRANS': 725} Chain breaks: 4 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 110 Chain: "C" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1412 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 1, 'TRANS': 205} Chain breaks: 3 Unresolved non-hydrogen bonds: 263 Unresolved non-hydrogen angles: 315 Unresolved non-hydrogen dihedrals: 220 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 10, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 138 Chain: "D" Number of atoms: 2438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2438 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 7, 'ASN:plan1': 5, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 127 Chain: "E" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 364 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 54 Unusual residues: {'NAG': 1, 'ZQY': 1} Inner-chain residues flagged as termini: ['pdbres="GLU A 902 "'] Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.05, per 1000 atoms: 0.56 Number of scatterers: 16068 At special positions: 0 Unit cell: (109.33, 123.213, 252.501, 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 109 16.00 O 2914 8.00 N 2787 7.00 C 10258 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 92 " distance=2.04 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 518 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 362 " distance=2.03 Simple disulfide: pdb=" SG CYS A 400 " - pdb=" SG CYS A 407 " distance=2.02 Simple disulfide: pdb=" SG CYS A 500 " - pdb=" SG CYS A 519 " distance=2.03 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 525 " - pdb=" SG CYS A 537 " distance=2.03 Simple disulfide: pdb=" SG CYS A 540 " - pdb=" SG CYS A 553 " distance=2.03 Simple disulfide: pdb=" SG CYS A 632 " - pdb=" SG CYS A 721 " distance=2.03 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 234 " - pdb=" SG CYS B 518 " distance=2.04 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 362 " distance=2.03 Simple disulfide: pdb=" SG CYS B 400 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 500 " - pdb=" SG CYS B 519 " distance=2.05 Simple disulfide: pdb=" SG CYS B 504 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 525 " - pdb=" SG CYS B 537 " distance=2.04 Simple disulfide: pdb=" SG CYS B 540 " - pdb=" SG CYS B 553 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 903 " - " ASN A 203 " " NAG B 902 " - " ASN B 203 " Time building additional restraints: 6.56 Conformation dependent library (CDL) restraints added in 2.5 seconds 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4020 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 21 sheets defined 39.6% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.31 Creating SS restraints... Processing helix chain 'A' and resid 59 through 74 Processing helix chain 'A' and resid 95 through 106 removed outlier: 3.883A pdb=" N LEU A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ASP A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N PHE A 105 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 157 removed outlier: 4.518A pdb=" N LEU A 157 " --> pdb=" O ASN A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 189 through 201 removed outlier: 4.131A pdb=" N LYS A 193 " --> pdb=" O PHE A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 231 removed outlier: 3.665A pdb=" N ARG A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 259 Processing helix chain 'A' and resid 272 through 285 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 325 through 333 removed outlier: 3.624A pdb=" N SER A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 353 Processing helix chain 'A' and resid 376 through 399 removed outlier: 4.335A pdb=" N MET A 379 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU A 399 " --> pdb=" O HIS A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 421 Processing helix chain 'A' and resid 566 through 591 removed outlier: 4.408A pdb=" N GLY A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) Proline residue: A 571 - end of helix Processing helix chain 'A' and resid 596 through 600 Processing helix chain 'A' and resid 604 through 624 removed outlier: 4.714A pdb=" N THR A 620 " --> pdb=" O CYS A 616 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N PHE A 621 " --> pdb=" O TYR A 617 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE A 622 " --> pdb=" O CYS A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 665 removed outlier: 4.063A pdb=" N LEU A 639 " --> pdb=" O ARG A 635 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLY A 640 " --> pdb=" O ARG A 636 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE A 643 " --> pdb=" O LEU A 639 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE A 657 " --> pdb=" O LYS A 653 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA A 664 " --> pdb=" O ILE A 660 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ARG A 665 " --> pdb=" O PHE A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 700 removed outlier: 3.841A pdb=" N GLN A 690 " --> pdb=" O LEU A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 748 Processing helix chain 'A' and resid 754 through 756 No H-bonds generated for 'chain 'A' and resid 754 through 756' Processing helix chain 'A' and resid 759 through 782 Proline residue: A 778 - end of helix Processing helix chain 'A' and resid 787 through 818 removed outlier: 4.091A pdb=" N SER A 797 " --> pdb=" O THR A 793 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA A 811 " --> pdb=" O GLY A 807 " (cutoff:3.500A) Proline residue: A 812 - end of helix Processing helix chain 'A' and resid 821 through 823 No H-bonds generated for 'chain 'A' and resid 821 through 823' Processing helix chain 'B' and resid 59 through 74 removed outlier: 3.613A pdb=" N ARG B 74 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 106 removed outlier: 5.037A pdb=" N ASP B 104 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N PHE B 105 " --> pdb=" O GLN B 101 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL B 106 " --> pdb=" O ALA B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 158 removed outlier: 3.624A pdb=" N LEU B 154 " --> pdb=" O GLN B 150 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU B 157 " --> pdb=" O ASN B 153 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N PHE B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 173 Processing helix chain 'B' and resid 189 through 202 removed outlier: 4.198A pdb=" N LYS B 193 " --> pdb=" O PHE B 189 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE B 202 " --> pdb=" O ILE B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 231 removed outlier: 3.554A pdb=" N ALA B 230 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG B 231 " --> pdb=" O GLU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 259 Processing helix chain 'B' and resid 272 through 284 Processing helix chain 'B' and resid 308 through 311 No H-bonds generated for 'chain 'B' and resid 308 through 311' Processing helix chain 'B' and resid 325 through 333 removed outlier: 3.794A pdb=" N SER B 329 " --> pdb=" O SER B 325 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER B 333 " --> pdb=" O SER B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 353 Processing helix chain 'B' and resid 376 through 399 removed outlier: 4.321A pdb=" N MET B 379 " --> pdb=" O SER B 376 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE B 380 " --> pdb=" O LYS B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 423 through 425 No H-bonds generated for 'chain 'B' and resid 423 through 425' Processing helix chain 'B' and resid 566 through 591 removed outlier: 4.590A pdb=" N GLY B 570 " --> pdb=" O ALA B 566 " (cutoff:3.500A) Proline residue: B 571 - end of helix Processing helix chain 'B' and resid 596 through 600 Processing helix chain 'B' and resid 605 through 623 removed outlier: 4.316A pdb=" N THR B 620 " --> pdb=" O CYS B 616 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE B 621 " --> pdb=" O TYR B 617 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE B 622 " --> pdb=" O CYS B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 659 removed outlier: 4.198A pdb=" N LEU B 639 " --> pdb=" O ARG B 635 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N GLY B 640 " --> pdb=" O ARG B 636 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS B 646 " --> pdb=" O ALA B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 700 removed outlier: 3.680A pdb=" N GLN B 690 " --> pdb=" O LEU B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 748 removed outlier: 3.883A pdb=" N GLY B 730 " --> pdb=" O SER B 727 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N THR B 743 " --> pdb=" O ALA B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 785 Proline residue: B 778 - end of helix removed outlier: 4.144A pdb=" N TYR B 781 " --> pdb=" O LEU B 777 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N SER B 785 " --> pdb=" O TYR B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 818 removed outlier: 3.822A pdb=" N VAL B 805 " --> pdb=" O SER B 801 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 811 " --> pdb=" O GLY B 807 " (cutoff:3.500A) Proline residue: B 812 - end of helix Processing helix chain 'C' and resid 7 through 30 Processing helix chain 'C' and resid 46 through 52 Processing helix chain 'C' and resid 208 through 215 removed outlier: 5.341A pdb=" N HIS C 213 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N CYS C 214 " --> pdb=" O LYS C 210 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N PHE C 215 " --> pdb=" O TRP C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 255 Processing helix chain 'C' and resid 271 through 280 removed outlier: 4.158A pdb=" N GLU C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 308 Processing helix chain 'C' and resid 331 through 350 removed outlier: 3.650A pdb=" N ASP C 341 " --> pdb=" O ASP C 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 25 Processing helix chain 'D' and resid 30 through 33 No H-bonds generated for 'chain 'D' and resid 30 through 33' Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'E' and resid 8 through 24 removed outlier: 4.114A pdb=" N ASN E 24 " --> pdb=" O LYS E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 43 removed outlier: 3.535A pdb=" N CYS E 41 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU E 42 " --> pdb=" O MET E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 58 No H-bonds generated for 'chain 'E' and resid 56 through 58' Processing sheet with id= A, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.507A pdb=" N LEU A 32 " --> pdb=" O GLY A 85 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N HIS A 87 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU A 34 " --> pdb=" O HIS A 87 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N LEU A 89 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLY A 36 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLY A 138 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N LEU A 37 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ILE A 140 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N GLY A 141 " --> pdb=" O PRO A 161 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ILE A 163 " --> pdb=" O GLY A 141 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 290 through 293 removed outlier: 7.489A pdb=" N TYR A 206 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N VAL A 267 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N SER A 208 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N PHE A 269 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL A 210 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N CYS A 234 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N THR A 209 " --> pdb=" O CYS A 234 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ALA A 236 " --> pdb=" O THR A 209 " (cutoff:3.500A) removed outlier: 12.944A pdb=" N ALA A 211 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 9.932A pdb=" N SER A 238 " --> pdb=" O ALA A 211 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 315 through 319 removed outlier: 3.631A pdb=" N GLY A 472 " --> pdb=" O ILE A 455 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N THR A 457 " --> pdb=" O LYS A 470 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LYS A 470 " --> pdb=" O THR A 457 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU A 459 " --> pdb=" O TYR A 468 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N TYR A 468 " --> pdb=" O LEU A 459 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 508 through 512 Processing sheet with id= E, first strand: chain 'A' and resid 544 through 546 Processing sheet with id= F, first strand: chain 'A' and resid 705 through 708 Processing sheet with id= G, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.620A pdb=" N LEU B 32 " --> pdb=" O GLY B 85 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N HIS B 87 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU B 34 " --> pdb=" O HIS B 87 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N LEU B 89 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLY B 36 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLY B 138 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N LEU B 37 " --> pdb=" O GLY B 138 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ILE B 140 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N GLY B 141 " --> pdb=" O PRO B 161 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ILE B 163 " --> pdb=" O GLY B 141 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 290 through 293 removed outlier: 7.546A pdb=" N TYR B 206 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N VAL B 267 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N SER B 208 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N PHE B 269 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL B 210 " --> pdb=" O PHE B 269 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N CYS B 234 " --> pdb=" O VAL B 207 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N THR B 209 " --> pdb=" O CYS B 234 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N ALA B 236 " --> pdb=" O THR B 209 " (cutoff:3.500A) removed outlier: 12.903A pdb=" N ALA B 211 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 10.045A pdb=" N SER B 238 " --> pdb=" O ALA B 211 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 315 through 319 removed outlier: 3.622A pdb=" N GLY B 472 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N THR B 457 " --> pdb=" O LYS B 470 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LYS B 470 " --> pdb=" O THR B 457 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU B 459 " --> pdb=" O TYR B 468 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N TYR B 468 " --> pdb=" O LEU B 459 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 508 through 511 Processing sheet with id= K, first strand: chain 'B' and resid 544 through 546 Processing sheet with id= L, first strand: chain 'B' and resid 705 through 708 Processing sheet with id= M, first strand: chain 'B' and resid 529 through 533 removed outlier: 6.824A pdb=" N THR B 536 " --> pdb=" O LEU B 532 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 319 through 323 removed outlier: 6.329A pdb=" N ILE C 264 " --> pdb=" O TYR C 320 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N HIS C 322 " --> pdb=" O ILE C 264 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU C 266 " --> pdb=" O HIS C 322 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA C 220 " --> pdb=" O LYS C 35 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 58 through 63 removed outlier: 7.350A pdb=" N ALA D 73 " --> pdb=" O TYR D 59 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N MET D 61 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL D 71 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N TRP D 63 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU D 69 " --> pdb=" O TRP D 63 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER D 74 " --> pdb=" O LYS D 78 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LYS D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N HIS D 91 " --> pdb=" O ILE D 81 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASP D 83 " --> pdb=" O LYS D 89 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LYS D 89 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 102 through 105 removed outlier: 6.230A pdb=" N ASN D 125 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL D 135 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 146 through 151 removed outlier: 6.830A pdb=" N SER D 160 " --> pdb=" O SER D 147 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N CYS D 149 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL D 158 " --> pdb=" O CYS D 149 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N PHE D 151 " --> pdb=" O GLN D 156 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N GLN D 156 " --> pdb=" O PHE D 151 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR D 178 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ASP D 170 " --> pdb=" O GLN D 176 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLN D 176 " --> pdb=" O ASP D 170 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 187 through 192 removed outlier: 6.912A pdb=" N GLY D 202 " --> pdb=" O MET D 188 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU D 190 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL D 200 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N LEU D 192 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LEU D 198 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN D 220 " --> pdb=" O LEU D 210 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ASP D 212 " --> pdb=" O CYS D 218 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N CYS D 218 " --> pdb=" O ASP D 212 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 229 through 234 removed outlier: 6.944A pdb=" N GLY D 244 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ILE D 232 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA D 242 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N PHE D 234 " --> pdb=" O ALA D 240 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ALA D 240 " --> pdb=" O PHE D 234 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS D 250 " --> pdb=" O TYR D 264 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N MET D 262 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ASP D 254 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLU D 260 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 293 through 298 removed outlier: 4.186A pdb=" N ASN D 293 " --> pdb=" O TYR D 289 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER D 275 " --> pdb=" O GLY D 288 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 46 through 51 removed outlier: 4.001A pdb=" N ARG D 46 " --> pdb=" O ASN D 340 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN D 340 " --> pdb=" O ARG D 46 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE D 338 " --> pdb=" O ARG D 48 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR D 50 " --> pdb=" O LEU D 336 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU D 336 " --> pdb=" O THR D 50 " (cutoff:3.500A) 688 hydrogen bonds defined for protein. 1851 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: 5.58 Time building geometry restraints manager: 7.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5051 1.34 - 1.46: 3879 1.46 - 1.58: 7363 1.58 - 1.71: 0 1.71 - 1.83: 141 Bond restraints: 16434 Sorted by residual: bond pdb=" C1 ZQY A 901 " pdb=" C2 ZQY A 901 " ideal model delta sigma weight residual 1.390 1.528 -0.138 2.00e-02 2.50e+03 4.78e+01 bond pdb=" C5 ZQY A 901 " pdb=" C6 ZQY A 901 " ideal model delta sigma weight residual 1.392 1.519 -0.127 2.00e-02 2.50e+03 4.06e+01 bond pdb=" C3 ZQY A 901 " pdb=" C4 ZQY A 901 " ideal model delta sigma weight residual 1.394 1.519 -0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" C9 ZQY A 901 " pdb=" N1 ZQY A 901 " ideal model delta sigma weight residual 1.337 1.446 -0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" N5 ZQY A 901 " pdb=" N6 ZQY A 901 " ideal model delta sigma weight residual 1.274 1.371 -0.097 2.00e-02 2.50e+03 2.34e+01 ... (remaining 16429 not shown) Histogram of bond angle deviations from ideal: 89.46 - 98.42: 3 98.42 - 107.38: 578 107.38 - 116.33: 10206 116.33 - 125.29: 11319 125.29 - 134.24: 287 Bond angle restraints: 22393 Sorted by residual: angle pdb=" N GLU A 712 " pdb=" CA GLU A 712 " pdb=" C GLU A 712 " ideal model delta sigma weight residual 109.15 99.20 9.95 1.44e+00 4.82e-01 4.78e+01 angle pdb=" CA PRO B 711 " pdb=" N PRO B 711 " pdb=" CD PRO B 711 " ideal model delta sigma weight residual 112.00 104.31 7.69 1.40e+00 5.10e-01 3.01e+01 angle pdb=" C GLU A 712 " pdb=" CA GLU A 712 " pdb=" CB GLU A 712 " ideal model delta sigma weight residual 110.67 118.62 -7.95 1.52e+00 4.33e-01 2.73e+01 angle pdb=" C ALA A 710 " pdb=" N PRO A 711 " pdb=" CA PRO A 711 " ideal model delta sigma weight residual 119.28 124.70 -5.42 1.10e+00 8.26e-01 2.42e+01 angle pdb=" CA ARG A 714 " pdb=" C ARG A 714 " pdb=" O ARG A 714 " ideal model delta sigma weight residual 120.55 115.53 5.02 1.06e+00 8.90e-01 2.24e+01 ... (remaining 22388 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 8858 17.93 - 35.85: 656 35.85 - 53.78: 109 53.78 - 71.70: 15 71.70 - 89.63: 16 Dihedral angle restraints: 9654 sinusoidal: 3436 harmonic: 6218 Sorted by residual: dihedral pdb=" CB CYS A 400 " pdb=" SG CYS A 400 " pdb=" SG CYS A 407 " pdb=" CB CYS A 407 " ideal model delta sinusoidal sigma weight residual 93.00 -177.37 -89.63 1 1.00e+01 1.00e-02 9.54e+01 dihedral pdb=" CB CYS B 540 " pdb=" SG CYS B 540 " pdb=" SG CYS B 553 " pdb=" CB CYS B 553 " ideal model delta sinusoidal sigma weight residual -86.00 -168.46 82.46 1 1.00e+01 1.00e-02 8.34e+01 dihedral pdb=" CB CYS A 234 " pdb=" SG CYS A 234 " pdb=" SG CYS A 518 " pdb=" CB CYS A 518 " ideal model delta sinusoidal sigma weight residual -86.00 -156.23 70.23 1 1.00e+01 1.00e-02 6.35e+01 ... (remaining 9651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 2457 0.105 - 0.211: 108 0.211 - 0.316: 8 0.316 - 0.421: 0 0.421 - 0.526: 1 Chirality restraints: 2574 Sorted by residual: chirality pdb=" C1 NAG A 903 " pdb=" ND2 ASN A 203 " pdb=" C2 NAG A 903 " pdb=" O5 NAG A 903 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 6.92e+00 chirality pdb=" CA GLU B 516 " pdb=" N GLU B 516 " pdb=" C GLU B 516 " pdb=" CB GLU B 516 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA PRO B 711 " pdb=" N PRO B 711 " pdb=" C PRO B 711 " pdb=" CB PRO B 711 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 2571 not shown) Planarity restraints: 2878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 903 " -0.164 2.00e-02 2.50e+03 1.36e-01 2.30e+02 pdb=" C7 NAG A 903 " 0.046 2.00e-02 2.50e+03 pdb=" C8 NAG A 903 " -0.121 2.00e-02 2.50e+03 pdb=" N2 NAG A 903 " 0.220 2.00e-02 2.50e+03 pdb=" O7 NAG A 903 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 902 " 0.073 2.00e-02 2.50e+03 5.99e-02 4.49e+01 pdb=" C7 NAG B 902 " -0.021 2.00e-02 2.50e+03 pdb=" C8 NAG B 902 " 0.055 2.00e-02 2.50e+03 pdb=" N2 NAG B 902 " -0.095 2.00e-02 2.50e+03 pdb=" O7 NAG B 902 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 710 " 0.097 5.00e-02 4.00e+02 1.43e-01 3.25e+01 pdb=" N PRO B 711 " -0.246 5.00e-02 4.00e+02 pdb=" CA PRO B 711 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO B 711 " 0.076 5.00e-02 4.00e+02 ... (remaining 2875 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2268 2.75 - 3.29: 15006 3.29 - 3.83: 24851 3.83 - 4.36: 28766 4.36 - 4.90: 51330 Nonbonded interactions: 122221 Sorted by model distance: nonbonded pdb=" OH TYR C 320 " pdb=" OD2 ASP C 341 " model vdw 2.213 2.440 nonbonded pdb=" O LEU B 686 " pdb=" OH TYR B 734 " model vdw 2.213 2.440 nonbonded pdb=" ND1 HIS D 142 " pdb=" OG SER D 161 " model vdw 2.233 2.520 nonbonded pdb=" O ALA A 630 " pdb=" OG1 THR A 633 " model vdw 2.235 2.440 nonbonded pdb=" O GLU B 508 " pdb=" NH1 ARG B 531 " model vdw 2.242 2.520 ... (remaining 122216 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 47 or (resid 48 and (name N or name CA or name \ C or name O or name CB )) or resid 49 through 358 or resid 360 through 419 or (r \ esid 420 and (name N or name CA or name C or name O or name CB )) or resid 421 t \ hrough 462 or resid 465 through 504 or (resid 505 through 506 and (name N or nam \ e CA or name C or name O or name CB )) or resid 507 through 512 or (resid 513 an \ d (name N or name CA or name C or name O or name CB )) or resid 514 through 549 \ or (resid 550 through 551 and (name N or name CA or name C or name O or name CB \ )) or resid 552 through 557 or (resid 558 through 559 and (name N or name CA or \ name C or name O or name CB )) or resid 560 or (resid 561 through 562 and (name \ N or name CA or name C or name O or name CB )) or resid 563 through 589 or (resi \ d 590 through 591 and (name N or name CA or name C or name O or name CB )) or re \ sid 592 through 598 or (resid 599 through 600 and (name N or name CA or name C o \ r name O or name CB )) or resid 601 through 602 or (resid 603 through 604 and (n \ ame N or name CA or name C or name O or name CB )) or resid 605 through 607 or ( \ resid 608 and (name N or name CA or name C or name O or name CB )) or resid 609 \ through 625 or (resid 626 and (name N or name CA or name C or name O or name CB \ )) or resid 627 through 640 or (resid 641 through 642 and (name N or name CA or \ name C or name O or name CB )) or resid 643 through 647 or (resid 648 through 64 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 650 through \ 654 or (resid 655 through 656 and (name N or name CA or name C or name O or name \ CB )) or resid 657 through 658 or (resid 659 through 661 and (name N or name CA \ or name C or name O or name CB )) or (resid 673 through 675 and (name N or name \ CA or name C or name O or name CB )) or resid 676 through 677 or (resid 678 and \ (name N or name CA or name C or name O or name CB )) or resid 679 through 681 o \ r (resid 682 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 83 through 687 or (resid 688 and (name N or name CA or name C or name O or name \ CB )) or resid 689 through 708 or (resid 709 through 710 and (name N or name CA \ or name C or name O or name CB )) or resid 711 through 713 or (resid 714 through \ 716 and (name N or name CA or name C or name O or name CB )) or resid 717 throu \ gh 721 or (resid 722 and (name N or name CA or name C or name O or name CB )) or \ resid 723 through 757 or (resid 758 through 759 and (name N or name CA or name \ C or name O or name CB )) or resid 760 through 765 or (resid 766 and (name N or \ name CA or name C or name O or name CB )) or resid 767 through 784 or (resid 785 \ and (name N or name CA or name C or name O or name CB )) or resid 786 through 8 \ 02 or (resid 803 and (name N or name CA or name C or name O or name CB )) or res \ id 804 through 817 or (resid 818 through 820 and (name N or name CA or name C or \ name O or name CB )) or resid 821 through 823 or resid 902 through 903)) selection = (chain 'B' and (resid 23 through 435 or (resid 436 and (name N or name CA or nam \ e C or name O or name CB )) or resid 437 through 475 or (resid 476 and (name N o \ r name CA or name C or name O or name CB )) or resid 477 through 505 or (resid 5 \ 06 and (name N or name CA or name C or name O or name CB )) or resid 507 through \ 590 or (resid 591 and (name N or name CA or name C or name O or name CB )) or r \ esid 592 through 714 or (resid 715 through 716 and (name N or name CA or name C \ or name O or name CB )) or resid 717 through 823 or resid 901 through 902)) } 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 individual isotropic 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: 4.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 19.250 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 43.870 Find NCS groups from input model: 0.890 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.138 16434 Z= 0.473 Angle : 0.774 9.951 22393 Z= 0.437 Chirality : 0.052 0.526 2574 Planarity : 0.007 0.143 2876 Dihedral : 13.112 87.771 5583 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer Outliers : 0.13 % 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: 0.41 (0.18), residues: 2120 helix: 1.72 (0.18), residues: 842 sheet: -0.20 (0.25), residues: 394 loop : -0.91 (0.20), residues: 884 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 143 time to evaluate : 1.894 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 145 average time/residue: 0.2868 time to fit residues: 63.2259 Evaluate side-chains 133 residues out of total 1791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 132 time to evaluate : 2.035 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1427 time to fit residues: 2.9674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 0.5980 chunk 160 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 123 optimal weight: 7.9990 chunk 192 optimal weight: 0.4980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN D 110 ASN D 125 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.0760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 16434 Z= 0.183 Angle : 0.498 7.439 22393 Z= 0.268 Chirality : 0.041 0.141 2574 Planarity : 0.005 0.076 2876 Dihedral : 4.766 73.548 2324 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 0.76 % 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: 0.52 (0.18), residues: 2120 helix: 1.84 (0.18), residues: 851 sheet: -0.11 (0.27), residues: 347 loop : -0.90 (0.20), residues: 922 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 135 time to evaluate : 2.191 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 139 average time/residue: 0.2868 time to fit residues: 61.1129 Evaluate side-chains 131 residues out of total 1791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 125 time to evaluate : 1.987 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1520 time to fit residues: 4.3987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 chunk 208 optimal weight: 6.9990 chunk 171 optimal weight: 6.9990 chunk 191 optimal weight: 0.0020 chunk 65 optimal weight: 0.5980 chunk 154 optimal weight: 1.9990 overall best weight: 1.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 GLN ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 GLN D 88 ASN D 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 16434 Z= 0.352 Angle : 0.583 8.449 22393 Z= 0.311 Chirality : 0.044 0.152 2574 Planarity : 0.005 0.066 2876 Dihedral : 4.896 60.945 2324 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.18), residues: 2120 helix: 1.64 (0.18), residues: 852 sheet: -0.22 (0.26), residues: 375 loop : -1.03 (0.20), residues: 893 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 1.942 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 135 average time/residue: 0.2788 time to fit residues: 58.3148 Evaluate side-chains 132 residues out of total 1791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 123 time to evaluate : 1.983 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1453 time to fit residues: 5.0485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 129 optimal weight: 0.0870 chunk 193 optimal weight: 0.9990 chunk 204 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 16434 Z= 0.188 Angle : 0.482 7.549 22393 Z= 0.259 Chirality : 0.041 0.138 2574 Planarity : 0.004 0.059 2876 Dihedral : 4.514 53.919 2324 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.47 (0.18), residues: 2120 helix: 1.84 (0.18), residues: 852 sheet: -0.18 (0.27), residues: 355 loop : -0.96 (0.19), residues: 913 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 133 time to evaluate : 2.036 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 138 average time/residue: 0.2795 time to fit residues: 59.3033 Evaluate side-chains 134 residues out of total 1791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 126 time to evaluate : 1.756 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1438 time to fit residues: 4.4939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 174 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 183 optimal weight: 0.1980 chunk 51 optimal weight: 0.7980 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 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 16434 Z= 0.320 Angle : 0.550 7.664 22393 Z= 0.295 Chirality : 0.043 0.157 2574 Planarity : 0.005 0.056 2876 Dihedral : 4.727 57.024 2324 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer Outliers : 0.57 % 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: 0.29 (0.18), residues: 2120 helix: 1.70 (0.18), residues: 852 sheet: -0.22 (0.26), residues: 375 loop : -1.12 (0.19), residues: 893 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 122 time to evaluate : 1.935 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 129 average time/residue: 0.2830 time to fit residues: 56.3264 Evaluate side-chains 125 residues out of total 1791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 121 time to evaluate : 1.871 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1473 time to fit residues: 3.6565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 3.9990 chunk 184 optimal weight: 0.0670 chunk 40 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 205 optimal weight: 0.9990 chunk 170 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 16434 Z= 0.181 Angle : 0.479 8.846 22393 Z= 0.256 Chirality : 0.040 0.138 2574 Planarity : 0.004 0.059 2876 Dihedral : 4.427 51.119 2324 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 0.70 % 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: 0.48 (0.18), residues: 2120 helix: 1.89 (0.19), residues: 853 sheet: -0.19 (0.26), residues: 366 loop : -1.01 (0.19), residues: 901 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 131 time to evaluate : 1.913 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 134 average time/residue: 0.2975 time to fit residues: 61.0001 Evaluate side-chains 132 residues out of total 1791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 126 time to evaluate : 1.801 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1426 time to fit residues: 3.9817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 172 optimal weight: 6.9990 chunk 114 optimal weight: 0.4980 chunk 204 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 126 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 16434 Z= 0.207 Angle : 0.490 8.181 22393 Z= 0.261 Chirality : 0.041 0.134 2574 Planarity : 0.004 0.055 2876 Dihedral : 4.396 49.046 2324 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.18), residues: 2120 helix: 1.89 (0.18), residues: 853 sheet: -0.17 (0.27), residues: 357 loop : -1.04 (0.19), residues: 910 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 129 time to evaluate : 1.990 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 133 average time/residue: 0.2803 time to fit residues: 57.6945 Evaluate side-chains 130 residues out of total 1791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 127 time to evaluate : 1.995 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1609 time to fit residues: 3.4568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 61 optimal weight: 0.3980 chunk 40 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 129 optimal weight: 9.9990 chunk 139 optimal weight: 0.0670 chunk 101 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 185 optimal weight: 4.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 16434 Z= 0.160 Angle : 0.462 7.628 22393 Z= 0.246 Chirality : 0.040 0.133 2574 Planarity : 0.004 0.057 2876 Dihedral : 4.200 43.692 2324 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.19), residues: 2120 helix: 1.99 (0.19), residues: 858 sheet: -0.18 (0.26), residues: 376 loop : -0.98 (0.20), residues: 886 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 135 time to evaluate : 1.857 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 137 average time/residue: 0.2656 time to fit residues: 57.1504 Evaluate side-chains 130 residues out of total 1791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 127 time to evaluate : 1.865 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1533 time to fit residues: 3.2960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 0.8980 chunk 178 optimal weight: 0.0040 chunk 190 optimal weight: 4.9990 chunk 114 optimal weight: 0.0070 chunk 82 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 180 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 overall best weight: 0.5610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 16434 Z= 0.148 Angle : 0.459 7.953 22393 Z= 0.244 Chirality : 0.040 0.135 2574 Planarity : 0.004 0.054 2876 Dihedral : 4.084 40.753 2324 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.19), residues: 2120 helix: 2.05 (0.19), residues: 857 sheet: -0.16 (0.26), residues: 378 loop : -0.95 (0.20), residues: 885 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 131 time to evaluate : 1.783 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 133 average time/residue: 0.2730 time to fit residues: 57.1732 Evaluate side-chains 127 residues out of total 1791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 124 time to evaluate : 1.828 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1766 time to fit residues: 3.3598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 211 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 chunk 103 optimal weight: 0.0470 chunk 133 optimal weight: 6.9990 overall best weight: 1.9284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.046 16434 Z= 0.384 Angle : 0.580 7.786 22393 Z= 0.309 Chirality : 0.044 0.150 2574 Planarity : 0.005 0.052 2876 Dihedral : 4.683 49.488 2324 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer Outliers : 0.13 % 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: 0.22 (0.18), residues: 2120 helix: 1.66 (0.18), residues: 855 sheet: -0.16 (0.25), residues: 384 loop : -1.25 (0.20), residues: 881 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 127 time to evaluate : 1.850 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 127 average time/residue: 0.2852 time to fit residues: 56.4549 Evaluate side-chains 127 residues out of total 1791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 125 time to evaluate : 2.009 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1590 time to fit residues: 3.2785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 3.9990 chunk 51 optimal weight: 0.0670 chunk 155 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 168 optimal weight: 8.9990 chunk 70 optimal weight: 0.5980 chunk 172 optimal weight: 6.9990 chunk 21 optimal weight: 0.0970 chunk 31 optimal weight: 0.3980 chunk 147 optimal weight: 4.9990 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.089384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.075796 restraints weight = 42534.677| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.22 r_work: 0.3047 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 16434 Z= 0.131 Angle : 0.461 8.369 22393 Z= 0.245 Chirality : 0.039 0.135 2574 Planarity : 0.004 0.058 2876 Dihedral : 4.162 41.414 2324 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 0.19 % 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: 0.61 (0.19), residues: 2120 helix: 2.04 (0.19), residues: 852 sheet: -0.24 (0.26), residues: 383 loop : -0.94 (0.20), residues: 885 =============================================================================== Job complete usr+sys time: 3183.61 seconds wall clock time: 58 minutes 45.34 seconds (3525.34 seconds total)