Starting phenix.real_space_refine on Tue Aug 6 16:42:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3x_17398/08_2024/8p3x_17398.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3x_17398/08_2024/8p3x_17398.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3x_17398/08_2024/8p3x_17398.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3x_17398/08_2024/8p3x_17398.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3x_17398/08_2024/8p3x_17398.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3x_17398/08_2024/8p3x_17398.cif" } resolution = 3.36 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= -0.001 sd= 0.048 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 121 5.16 5 C 11142 2.51 5 N 2749 2.21 5 O 3023 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 453": "NH1" <-> "NH2" Residue "A GLU 486": "OE1" <-> "OE2" Residue "A GLU 627": "OE1" <-> "OE2" Residue "A GLU 705": "OE1" <-> "OE2" Residue "A GLU 813": "OE1" <-> "OE2" Residue "B ARG 453": "NH1" <-> "NH2" Residue "B GLU 486": "OE1" <-> "OE2" Residue "B GLU 524": "OE1" <-> "OE2" Residue "B GLU 550": "OE1" <-> "OE2" Residue "B GLU 705": "OE1" <-> "OE2" Residue "C ARG 453": "NH1" <-> "NH2" Residue "C GLU 486": "OE1" <-> "OE2" Residue "C GLU 627": "OE1" <-> "OE2" Residue "C GLU 705": "OE1" <-> "OE2" Residue "D ARG 453": "NH1" <-> "NH2" Residue "D GLU 486": "OE1" <-> "OE2" Residue "D GLU 570": "OE1" <-> "OE2" Residue "D GLU 705": "OE1" <-> "OE2" Residue "E GLU 126": "OE1" <-> "OE2" Residue "E GLU 191": "OE1" <-> "OE2" Residue "F GLU 95": "OE1" <-> "OE2" Residue "F GLU 126": "OE1" <-> "OE2" Residue "F GLU 191": "OE1" <-> "OE2" Residue "G GLU 56": "OE1" <-> "OE2" Residue "G GLU 70": "OE1" <-> "OE2" Residue "G GLU 126": "OE1" <-> "OE2" Residue "H GLU 56": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 17035 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2910 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 398, 2899 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 386} Chain breaks: 4 Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 115 Conformer: "B" Number of residues, atoms: 398, 2899 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 386} Chain breaks: 4 Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 115 bond proxies already assigned to first conformer: 2950 Chain: "B" Number of atoms: 2886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 2886 Classifications: {'peptide': 397} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 384} Chain breaks: 4 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 124 Chain: "C" Number of atoms: 2881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2881 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 384} Chain breaks: 4 Unresolved non-hydrogen bonds: 231 Unresolved non-hydrogen angles: 272 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 124 Chain: "D" Number of atoms: 2883 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 395, 2872 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 382} Chain breaks: 3 Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 265 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 116 Conformer: "B" Number of residues, atoms: 395, 2872 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 382} Chain breaks: 3 Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 265 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 116 bond proxies already assigned to first conformer: 2925 Chain: "E" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1372 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1358 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "G" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1372 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1373 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N APHE A 574 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 574 " occ=0.50 residue: pdb=" N APHE D 574 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE D 574 " occ=0.50 Time building chain proxies: 11.44, per 1000 atoms: 0.67 Number of scatterers: 17035 At special positions: 0 Unit cell: (115.64, 144.55, 145.996, 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 121 16.00 O 3023 8.00 N 2749 7.00 C 11142 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.00 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.01 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.05 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.04 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.05 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.04 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.04 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.05 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.38 Conformation dependent library (CDL) restraints added in 4.1 seconds 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4192 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 28 sheets defined 60.8% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 416 through 419 removed outlier: 3.839A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 423 through 437 removed outlier: 3.634A pdb=" N ASP A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 469 Processing helix chain 'A' and resid 482 through 489 removed outlier: 3.790A pdb=" N VAL A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.842A pdb=" N LEU A 518 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 546 Processing helix chain 'A' and resid 547 through 551 Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 628 Processing helix chain 'A' and resid 635 through 642 Processing helix chain 'A' and resid 653 through 661 Processing helix chain 'A' and resid 664 through 677 Processing helix chain 'A' and resid 685 through 695 Processing helix chain 'A' and resid 706 through 715 Processing helix chain 'A' and resid 742 through 757 removed outlier: 3.600A pdb=" N LEU A 748 " --> pdb=" O THR A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 768 Processing helix chain 'A' and resid 788 through 820 removed outlier: 3.635A pdb=" N VAL A 792 " --> pdb=" O SER A 788 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N GLY A 794 " --> pdb=" O SER A 790 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL A 795 " --> pdb=" O ASN A 791 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 423 through 437 removed outlier: 3.673A pdb=" N ASP B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 482 through 488 removed outlier: 3.780A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.647A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 546 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 626 Processing helix chain 'B' and resid 635 through 642 Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 664 through 677 Processing helix chain 'B' and resid 685 through 695 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 742 through 757 removed outlier: 3.639A pdb=" N LEU B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 769 through 771 No H-bonds generated for 'chain 'B' and resid 769 through 771' Processing helix chain 'B' and resid 792 through 822 removed outlier: 3.548A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B 822 " --> pdb=" O SER B 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 417 through 419 No H-bonds generated for 'chain 'C' and resid 417 through 419' Processing helix chain 'C' and resid 423 through 437 removed outlier: 3.615A pdb=" N ASP C 427 " --> pdb=" O GLY C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 489 removed outlier: 3.764A pdb=" N VAL C 488 " --> pdb=" O VAL C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 522 through 546 removed outlier: 3.531A pdb=" N TRP C 526 " --> pdb=" O ALA C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 551 removed outlier: 3.669A pdb=" N GLU C 550 " --> pdb=" O SER C 547 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TRP C 551 " --> pdb=" O PRO C 548 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 547 through 551' Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 628 removed outlier: 3.567A pdb=" N ARG C 628 " --> pdb=" O LEU C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 642 Processing helix chain 'C' and resid 653 through 661 Processing helix chain 'C' and resid 664 through 677 Processing helix chain 'C' and resid 685 through 695 Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 742 through 757 removed outlier: 3.652A pdb=" N LEU C 748 " --> pdb=" O THR C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 767 Processing helix chain 'C' and resid 792 through 821 removed outlier: 3.763A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 415 Processing helix chain 'D' and resid 416 through 419 removed outlier: 4.014A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.622A pdb=" N ASP D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 488 removed outlier: 3.769A pdb=" N VAL D 488 " --> pdb=" O VAL D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.845A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 545 Processing helix chain 'D' and resid 572 through 585 removed outlier: 3.706A pdb=" N TRP D 578 " --> pdb=" O BPHE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 624 Processing helix chain 'D' and resid 636 through 642 Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 664 through 677 Processing helix chain 'D' and resid 685 through 695 Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 742 through 757 removed outlier: 3.503A pdb=" N ASN D 747 " --> pdb=" O GLY D 743 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU D 748 " --> pdb=" O THR D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 788 through 823 removed outlier: 3.798A pdb=" N VAL D 792 " --> pdb=" O SER D 788 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLY D 794 " --> pdb=" O SER D 790 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL D 795 " --> pdb=" O ASN D 791 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS D 823 " --> pdb=" O ARG D 819 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 30 Processing helix chain 'E' and resid 93 through 104 Processing helix chain 'E' and resid 105 through 124 Processing helix chain 'E' and resid 133 through 160 removed outlier: 3.799A pdb=" N SER E 137 " --> pdb=" O ASN E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 210 Processing helix chain 'F' and resid 6 through 28 Processing helix chain 'F' and resid 93 through 104 Processing helix chain 'F' and resid 105 through 127 removed outlier: 3.968A pdb=" N GLU F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 160 Processing helix chain 'F' and resid 177 through 209 Processing helix chain 'G' and resid 7 through 30 removed outlier: 3.692A pdb=" N LEU G 11 " --> pdb=" O GLY G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 104 Processing helix chain 'G' and resid 105 through 127 removed outlier: 4.113A pdb=" N GLU G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N PHE G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 161 Processing helix chain 'G' and resid 177 through 210 Processing helix chain 'H' and resid 6 through 30 removed outlier: 3.931A pdb=" N MET H 10 " --> pdb=" O ARG H 6 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU H 11 " --> pdb=" O GLY H 7 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 104 Processing helix chain 'H' and resid 105 through 124 Processing helix chain 'H' and resid 133 through 161 removed outlier: 3.582A pdb=" N ALA H 161 " --> pdb=" O ILE H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 209 removed outlier: 3.967A pdb=" N TYR H 181 " --> pdb=" O GLY H 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 394 through 399 Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA3, first strand: chain 'A' and resid 451 through 453 removed outlier: 3.611A pdb=" N ALA A 452 " --> pdb=" O ASN A 461 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 490 through 491 Processing sheet with id=AA5, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.469A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.229A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.469A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.229A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 394 through 399 Processing sheet with id=AA8, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA9, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AB1, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.475A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.190A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.475A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.190A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 394 through 399 Processing sheet with id=AB4, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB5, first strand: chain 'C' and resid 490 through 491 Processing sheet with id=AB6, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.485A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.485A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 395 through 399 removed outlier: 6.701A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC1, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AC2, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.408A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.174A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.408A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.174A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 34 through 38 Processing sheet with id=AC5, first strand: chain 'F' and resid 34 through 35 removed outlier: 4.129A pdb=" N SER F 175 " --> pdb=" O TYR F 35 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 37 through 38 Processing sheet with id=AC7, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.767A pdb=" N LYS F 78 " --> pdb=" O THR F 66 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 77 through 79 Processing sheet with id=AC9, first strand: chain 'H' and resid 36 through 38 Processing sheet with id=AD1, first strand: chain 'H' and resid 65 through 67 1124 hydrogen bonds defined for protein. 3282 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: 5.39 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: 1.17 - 1.31: 2640 1.31 - 1.44: 5000 1.44 - 1.57: 9588 1.57 - 1.70: 0 1.70 - 1.83: 194 Bond restraints: 17422 Sorted by residual: bond pdb=" C APHE D 574 " pdb=" N ASN D 575 " ideal model delta sigma weight residual 1.335 1.463 -0.127 1.38e-02 5.25e+03 8.54e+01 bond pdb=" C BPHE D 574 " pdb=" N ASN D 575 " ideal model delta sigma weight residual 1.334 1.468 -0.133 1.46e-02 4.69e+03 8.36e+01 bond pdb=" C ASN A 709 " pdb=" O ASN A 709 " ideal model delta sigma weight residual 1.237 1.306 -0.069 1.16e-02 7.43e+03 3.55e+01 bond pdb=" CA SER A 592 " pdb=" CB SER A 592 " ideal model delta sigma weight residual 1.535 1.472 0.063 1.21e-02 6.83e+03 2.68e+01 bond pdb=" C ILE A 573 " pdb=" N APHE A 574 " ideal model delta sigma weight residual 1.335 1.404 -0.070 1.36e-02 5.41e+03 2.62e+01 ... (remaining 17417 not shown) Histogram of bond angle deviations from ideal: 97.91 - 105.27: 288 105.27 - 112.63: 9070 112.63 - 119.98: 8941 119.98 - 127.34: 5218 127.34 - 134.70: 143 Bond angle restraints: 23660 Sorted by residual: angle pdb=" N ILE A 712 " pdb=" CA ILE A 712 " pdb=" CB ILE A 712 " ideal model delta sigma weight residual 110.54 99.22 11.32 1.36e+00 5.41e-01 6.93e+01 angle pdb=" N GLU A 772 " pdb=" CA GLU A 772 " pdb=" C GLU A 772 " ideal model delta sigma weight residual 113.61 102.50 11.11 1.50e+00 4.44e-01 5.48e+01 angle pdb=" N ASP C 590 " pdb=" CA ASP C 590 " pdb=" C ASP C 590 " ideal model delta sigma weight residual 113.88 105.69 8.19 1.23e+00 6.61e-01 4.44e+01 angle pdb=" N LEU C 803 " pdb=" CA LEU C 803 " pdb=" C LEU C 803 " ideal model delta sigma weight residual 111.82 104.39 7.43 1.16e+00 7.43e-01 4.10e+01 angle pdb=" N LEU D 620 " pdb=" CA LEU D 620 " pdb=" C LEU D 620 " ideal model delta sigma weight residual 111.07 104.25 6.82 1.07e+00 8.73e-01 4.06e+01 ... (remaining 23655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 8930 17.77 - 35.53: 878 35.53 - 53.30: 152 53.30 - 71.06: 20 71.06 - 88.83: 13 Dihedral angle restraints: 9993 sinusoidal: 3435 harmonic: 6558 Sorted by residual: dihedral pdb=" CB CYS F 40 " pdb=" SG CYS F 40 " pdb=" SG CYS F 68 " pdb=" CB CYS F 68 " ideal model delta sinusoidal sigma weight residual 93.00 24.05 68.95 1 1.00e+01 1.00e-02 6.15e+01 dihedral pdb=" CB CYS G 40 " pdb=" SG CYS G 40 " pdb=" SG CYS G 68 " pdb=" CB CYS G 68 " ideal model delta sinusoidal sigma weight residual 93.00 38.89 54.11 1 1.00e+01 1.00e-02 3.97e+01 dihedral pdb=" CB CYS E 40 " pdb=" SG CYS E 40 " pdb=" SG CYS E 68 " pdb=" CB CYS E 68 " ideal model delta sinusoidal sigma weight residual 93.00 39.54 53.46 1 1.00e+01 1.00e-02 3.88e+01 ... (remaining 9990 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 921 0.065 - 0.130: 1006 0.130 - 0.194: 628 0.194 - 0.259: 177 0.259 - 0.324: 13 Chirality restraints: 2745 Sorted by residual: chirality pdb=" CA ILE A 712 " pdb=" N ILE A 712 " pdb=" C ILE A 712 " pdb=" CB ILE A 712 " both_signs ideal model delta sigma weight residual False 2.43 2.76 -0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CA GLU A 710 " pdb=" N GLU A 710 " pdb=" C GLU A 710 " pdb=" CB GLU A 710 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.31 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CA CYS C 589 " pdb=" N CYS C 589 " pdb=" C CYS C 589 " pdb=" CB CYS C 589 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 2742 not shown) Planarity restraints: 2906 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA BPHE D 574 " -0.036 2.00e-02 2.50e+03 6.87e-02 4.72e+01 pdb=" C BPHE D 574 " 0.119 2.00e-02 2.50e+03 pdb=" O BPHE D 574 " -0.046 2.00e-02 2.50e+03 pdb=" N ASN D 575 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 819 " 0.569 9.50e-02 1.11e+02 2.55e-01 3.97e+01 pdb=" NE ARG C 819 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG C 819 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG C 819 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 819 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 420 " 0.520 9.50e-02 1.11e+02 2.33e-01 3.32e+01 pdb=" NE ARG B 420 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ARG B 420 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 420 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 420 " 0.019 2.00e-02 2.50e+03 ... (remaining 2903 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4188 2.77 - 3.30: 17633 3.30 - 3.83: 27176 3.83 - 4.37: 34067 4.37 - 4.90: 54990 Nonbonded interactions: 138054 Sorted by model distance: nonbonded pdb=" O LYS E 129 " pdb=" OG1 THR E 130 " model vdw 2.236 3.040 nonbonded pdb=" O SER E 104 " pdb=" N ILE E 106 " model vdw 2.250 3.120 nonbonded pdb=" N VAL D 395 " pdb=" O LYS D 439 " model vdw 2.261 3.120 nonbonded pdb=" O ASP B 427 " pdb=" OE1 GLU B 431 " model vdw 2.291 3.040 nonbonded pdb=" O ASP A 427 " pdb=" OE1 GLU A 431 " model vdw 2.294 3.040 ... (remaining 138049 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 549 or (resid 550 and (name N or name CA or na \ me C or name O or name CB )) or resid 551 through 573 or resid 575 through 593 o \ r (resid 594 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 95 through 626 or resid 635 through 773 or resid 785 through 812 or (resid 813 a \ nd (name N or name CA or name C or name O or name CB )) or resid 814 through 818 \ or (resid 819 through 823 and (name N or name CA or name C or name O or name CB \ )))) selection = (chain 'B' and (resid 393 through 506 or (resid 511 and (name N or name CA or na \ me C or name O or name CB )) or resid 512 through 549 or (resid 550 and (name N \ or name CA or name C or name O or name CB )) or resid 551 or (resid 569 and (nam \ e N or name CA or name C or name O or name CB )) or resid 570 through 573 or res \ id 575 or (resid 576 and (name N or name CA or name C or name O or name CB )) or \ resid 577 through 593 or (resid 594 and (name N or name CA or name C or name O \ or name CB )) or resid 595 through 626 or resid 635 through 773 or resid 785 thr \ ough 823)) selection = (chain 'C' and (resid 393 through 573 or resid 575 or (resid 576 and (name N or \ name CA or name C or name O or name CB )) or resid 577 through 626 or resid 635 \ through 812 or (resid 813 and (name N or name CA or name C or name O or name CB \ )) or resid 814 through 818 or (resid 819 through 823 and (name N or name CA or \ name C or name O or name CB )))) selection = (chain 'D' and (resid 393 through 506 or resid 511 through 549 or (resid 550 and \ (name N or name CA or name C or name O or name CB )) or resid 551 or (resid 569 \ and (name N or name CA or name C or name O or name CB )) or resid 570 through 5 \ 73 or resid 575 or (resid 576 and (name N or name CA or name C or name O or name \ CB )) or resid 577 through 593 or (resid 594 and (name N or name CA or name C o \ r name O or name CB )) or resid 595 through 823)) } ncs_group { reference = (chain 'E' and (resid 5 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 42 or (resid 56 and (name N or name \ CA or name C or name O or name CB )) or resid 57 through 84 or resid 93 through \ 161 or resid 173 through 210)) selection = (chain 'F' and (resid 5 through 42 or resid 56 through 84 or resid 93 through 21 \ 0)) selection = (chain 'G' and (resid 5 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 42 or (resid 56 and (name N or name \ CA or name C or name O or name CB )) or resid 57 through 84 or resid 93 through \ 161 or resid 173 through 210)) selection = (chain 'H' and (resid 5 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 42 or (resid 56 and (name N or name \ CA or name C or name O or name CB )) or resid 57 through 161 or resid 173 throu \ gh 210)) } 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=0.50 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: 1.840 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: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 48.760 Find NCS groups from input model: 0.860 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 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 : 0.013 0.133 17422 Z= 0.838 Angle : 1.656 11.319 23660 Z= 1.252 Chirality : 0.115 0.324 2745 Planarity : 0.014 0.255 2906 Dihedral : 14.277 88.829 5765 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.36 % Favored : 95.41 % Rotamer: Outliers : 1.68 % Allowed : 7.13 % Favored : 91.20 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 22.64 % 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: -1.65 (0.15), residues: 2229 helix: -0.38 (0.12), residues: 1304 sheet: -1.98 (0.37), residues: 145 loop : -2.01 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.005 TRP A 767 HIS 0.009 0.002 HIS E 60 PHE 0.032 0.004 PHE A 667 TYR 0.041 0.004 TYR A 647 ARG 0.014 0.001 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 405 time to evaluate : 2.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 590 ASP cc_start: 0.8956 (p0) cc_final: 0.8645 (p0) REVERT: A 594 ARG cc_start: 0.9599 (mtm-85) cc_final: 0.9316 (mtp85) REVERT: A 651 ASP cc_start: 0.3695 (p0) cc_final: 0.3107 (p0) REVERT: A 674 MET cc_start: 0.5429 (mtm) cc_final: 0.4769 (mtt) REVERT: A 819 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8749 (ptm-80) REVERT: C 633 ILE cc_start: -0.0215 (OUTLIER) cc_final: -0.0891 (pt) REVERT: D 519 ASP cc_start: 0.9464 (m-30) cc_final: 0.9203 (m-30) REVERT: E 78 LYS cc_start: 0.9264 (pttt) cc_final: 0.8878 (pttm) REVERT: E 81 ASP cc_start: 0.9271 (t0) cc_final: 0.9004 (p0) REVERT: E 192 MET cc_start: 0.8857 (mtt) cc_final: 0.8582 (mmt) REVERT: E 200 MET cc_start: 0.9334 (mtm) cc_final: 0.9101 (mtm) REVERT: F 24 MET cc_start: 0.9363 (tpt) cc_final: 0.9076 (tpt) REVERT: F 99 ARG cc_start: 0.9004 (tpp80) cc_final: 0.8778 (mmm-85) REVERT: F 117 MET cc_start: 0.8831 (mmm) cc_final: 0.8559 (mmm) REVERT: F 192 MET cc_start: 0.8424 (mtt) cc_final: 0.8077 (mmt) REVERT: F 207 GLN cc_start: 0.9419 (tt0) cc_final: 0.9028 (tm-30) REVERT: G 10 MET cc_start: 0.8778 (tpt) cc_final: 0.8424 (tpp) REVERT: G 24 MET cc_start: 0.8924 (tpt) cc_final: 0.8373 (tpt) REVERT: G 99 ARG cc_start: 0.9318 (mtt-85) cc_final: 0.8795 (mtm-85) REVERT: H 24 MET cc_start: 0.9238 (tpt) cc_final: 0.9009 (tpt) REVERT: H 58 MET cc_start: 0.9375 (mmp) cc_final: 0.9128 (mmp) REVERT: H 95 GLU cc_start: 0.9545 (tm-30) cc_final: 0.9264 (pm20) outliers start: 28 outliers final: 6 residues processed: 425 average time/residue: 0.3554 time to fit residues: 211.9837 Evaluate side-chains 246 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 238 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 819 ARG Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 620 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain F residue 58 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 0.9990 chunk 169 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 175 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 chunk 203 optimal weight: 0.0370 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN B 569 ASN B 619 ASN D 461 ASN D 619 ASN E 9 GLN E 82 HIS E 160 ASN F 82 HIS F 132 HIS F 205 HIS G 9 GLN G 205 HIS H 79 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6560 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17422 Z= 0.193 Angle : 0.618 11.544 23660 Z= 0.331 Chirality : 0.042 0.266 2745 Planarity : 0.004 0.041 2906 Dihedral : 4.661 56.788 2451 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.16 % Allowed : 14.79 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.64 % 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: 0.93 (0.18), residues: 2229 helix: 1.99 (0.14), residues: 1325 sheet: -1.51 (0.38), residues: 154 loop : -1.47 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 671 HIS 0.005 0.001 HIS F 82 PHE 0.014 0.001 PHE G 73 TYR 0.015 0.001 TYR D 469 ARG 0.007 0.001 ARG H 37 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 290 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 590 ASP cc_start: 0.8761 (p0) cc_final: 0.8436 (p0) REVERT: A 591 ILE cc_start: 0.9153 (tp) cc_final: 0.8896 (pt) REVERT: A 594 ARG cc_start: 0.9615 (mtm-85) cc_final: 0.9320 (mtp85) REVERT: A 674 MET cc_start: 0.5805 (mtm) cc_final: 0.5226 (mtt) REVERT: D 519 ASP cc_start: 0.9247 (m-30) cc_final: 0.9027 (m-30) REVERT: D 590 ASP cc_start: 0.8925 (t70) cc_final: 0.8672 (t0) REVERT: D 708 MET cc_start: 0.5460 (mpp) cc_final: 0.5034 (mpp) REVERT: E 56 GLU cc_start: 0.8949 (pt0) cc_final: 0.8547 (pp20) REVERT: E 78 LYS cc_start: 0.9124 (pttt) cc_final: 0.8921 (pttm) REVERT: E 81 ASP cc_start: 0.9257 (t0) cc_final: 0.9006 (p0) REVERT: E 151 ILE cc_start: 0.9610 (OUTLIER) cc_final: 0.9391 (tt) REVERT: E 176 TYR cc_start: 0.8410 (m-80) cc_final: 0.8050 (m-80) REVERT: E 195 VAL cc_start: 0.9037 (OUTLIER) cc_final: 0.8794 (t) REVERT: F 10 MET cc_start: 0.8744 (mmm) cc_final: 0.8083 (tpp) REVERT: F 58 MET cc_start: 0.9370 (tpp) cc_final: 0.9063 (mmp) REVERT: F 99 ARG cc_start: 0.8938 (tpp80) cc_final: 0.8678 (mmm-85) REVERT: F 160 ASN cc_start: 0.8681 (m-40) cc_final: 0.8464 (m110) REVERT: F 174 TYR cc_start: 0.8479 (p90) cc_final: 0.7440 (p90) REVERT: F 185 LEU cc_start: 0.9041 (tp) cc_final: 0.8840 (tp) REVERT: F 192 MET cc_start: 0.8465 (mtt) cc_final: 0.8205 (mmp) REVERT: F 207 GLN cc_start: 0.9293 (tt0) cc_final: 0.8784 (tm-30) REVERT: G 6 ARG cc_start: 0.8021 (tpt170) cc_final: 0.7293 (tpt170) REVERT: G 24 MET cc_start: 0.9120 (tpt) cc_final: 0.8434 (tpt) REVERT: G 99 ARG cc_start: 0.9160 (mtt-85) cc_final: 0.8681 (mtm180) REVERT: H 31 ASP cc_start: 0.8631 (m-30) cc_final: 0.8426 (m-30) REVERT: H 95 GLU cc_start: 0.9526 (tm-30) cc_final: 0.9253 (pm20) outliers start: 36 outliers final: 16 residues processed: 312 average time/residue: 0.3081 time to fit residues: 140.7065 Evaluate side-chains 254 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 236 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 199 HIS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 150 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 20.0000 chunk 63 optimal weight: 10.0000 chunk 169 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 203 optimal weight: 0.9990 chunk 220 optimal weight: 3.9990 chunk 181 optimal weight: 0.8980 chunk 202 optimal weight: 0.9990 chunk 69 optimal weight: 50.0000 chunk 163 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 ASN B 619 ASN D 619 ASN E 9 GLN E 72 ASN F 149 ASN F 205 HIS G 205 HIS H 149 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17422 Z= 0.296 Angle : 0.620 12.452 23660 Z= 0.328 Chirality : 0.042 0.230 2745 Planarity : 0.004 0.039 2906 Dihedral : 4.049 52.258 2435 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.17 % Allowed : 16.17 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.64 % 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: 1.58 (0.19), residues: 2229 helix: 2.55 (0.15), residues: 1329 sheet: -1.26 (0.39), residues: 167 loop : -1.30 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 551 HIS 0.008 0.001 HIS E 82 PHE 0.015 0.002 PHE D 541 TYR 0.015 0.001 TYR D 732 ARG 0.006 0.001 ARG B 586 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 242 time to evaluate : 1.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 594 ARG cc_start: 0.9643 (mtm-85) cc_final: 0.9355 (mtp85) REVERT: A 674 MET cc_start: 0.5790 (mtm) cc_final: 0.5248 (mtt) REVERT: D 569 ASN cc_start: 0.7830 (p0) cc_final: 0.7553 (p0) REVERT: D 590 ASP cc_start: 0.8895 (t70) cc_final: 0.8616 (t0) REVERT: E 10 MET cc_start: 0.8700 (mmm) cc_final: 0.8359 (tpp) REVERT: E 56 GLU cc_start: 0.9026 (pt0) cc_final: 0.8641 (pp20) REVERT: E 151 ILE cc_start: 0.9595 (OUTLIER) cc_final: 0.9317 (tt) REVERT: E 160 ASN cc_start: 0.8756 (m-40) cc_final: 0.8526 (t0) REVERT: F 110 LEU cc_start: 0.9008 (tp) cc_final: 0.8673 (tp) REVERT: F 160 ASN cc_start: 0.8715 (m-40) cc_final: 0.8404 (m110) REVERT: F 192 MET cc_start: 0.8524 (mtt) cc_final: 0.8256 (mmp) REVERT: F 207 GLN cc_start: 0.9245 (tt0) cc_final: 0.8820 (tm-30) REVERT: G 10 MET cc_start: 0.9080 (mmm) cc_final: 0.8698 (tpp) REVERT: G 99 ARG cc_start: 0.9178 (mtt-85) cc_final: 0.8643 (mtt180) REVERT: H 24 MET cc_start: 0.9290 (tpt) cc_final: 0.9040 (tpp) REVERT: H 31 ASP cc_start: 0.8641 (m-30) cc_final: 0.8356 (m-30) REVERT: H 35 TYR cc_start: 0.8380 (m-80) cc_final: 0.8015 (m-80) REVERT: H 95 GLU cc_start: 0.9571 (tm-30) cc_final: 0.9273 (pm20) outliers start: 53 outliers final: 30 residues processed: 281 average time/residue: 0.2982 time to fit residues: 123.7370 Evaluate side-chains 249 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 218 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 199 HIS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 158 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 2.9990 chunk 153 optimal weight: 0.5980 chunk 105 optimal weight: 20.0000 chunk 22 optimal weight: 30.0000 chunk 97 optimal weight: 0.6980 chunk 136 optimal weight: 0.7980 chunk 204 optimal weight: 0.6980 chunk 216 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 193 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 ASN B 619 ASN C 412 HIS D 619 ASN F 205 HIS H 149 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17422 Z= 0.169 Angle : 0.575 11.712 23660 Z= 0.299 Chirality : 0.040 0.179 2745 Planarity : 0.003 0.042 2906 Dihedral : 3.882 39.642 2435 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.81 % Allowed : 17.49 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.64 % 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: 1.83 (0.19), residues: 2229 helix: 2.71 (0.14), residues: 1342 sheet: -1.07 (0.40), residues: 167 loop : -1.21 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP D 671 HIS 0.021 0.002 HIS G 205 PHE 0.016 0.001 PHE G 73 TYR 0.032 0.001 TYR A 732 ARG 0.007 0.001 ARG G 37 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 254 time to evaluate : 1.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 594 ARG cc_start: 0.9623 (mtm-85) cc_final: 0.9349 (mtp85) REVERT: A 674 MET cc_start: 0.5655 (mtm) cc_final: 0.5114 (mtt) REVERT: B 755 GLU cc_start: 0.3955 (tp30) cc_final: 0.3557 (tp30) REVERT: C 811 LEU cc_start: 0.9273 (mt) cc_final: 0.9066 (mm) REVERT: D 590 ASP cc_start: 0.8889 (t70) cc_final: 0.8633 (t0) REVERT: D 721 MET cc_start: 0.6203 (ppp) cc_final: 0.5544 (ppp) REVERT: E 151 ILE cc_start: 0.9560 (OUTLIER) cc_final: 0.9315 (tt) REVERT: F 58 MET cc_start: 0.9322 (tpp) cc_final: 0.9059 (mmp) REVERT: F 110 LEU cc_start: 0.8911 (tp) cc_final: 0.8600 (tp) REVERT: F 185 LEU cc_start: 0.9022 (tp) cc_final: 0.8794 (tp) REVERT: F 192 MET cc_start: 0.8453 (mtt) cc_final: 0.8206 (mmp) REVERT: F 207 GLN cc_start: 0.9137 (tt0) cc_final: 0.8729 (tm-30) REVERT: G 69 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8408 (pp) REVERT: G 99 ARG cc_start: 0.9152 (mtt-85) cc_final: 0.8684 (mtm180) REVERT: H 35 TYR cc_start: 0.8268 (m-80) cc_final: 0.8030 (m-80) REVERT: H 95 GLU cc_start: 0.9582 (tm-30) cc_final: 0.9275 (pm20) outliers start: 47 outliers final: 28 residues processed: 287 average time/residue: 0.3062 time to fit residues: 130.2002 Evaluate side-chains 253 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 223 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 594 ARG Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 199 HIS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 150 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 161 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 184 optimal weight: 1.9990 chunk 149 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 110 optimal weight: 20.0000 chunk 194 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN B 569 ASN B 587 GLN B 619 ASN D 791 ASN ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 17422 Z= 0.530 Angle : 0.748 11.438 23660 Z= 0.394 Chirality : 0.045 0.216 2745 Planarity : 0.004 0.044 2906 Dihedral : 4.334 37.353 2435 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.19 % Allowed : 17.84 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.64 % 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: 1.44 (0.19), residues: 2229 helix: 2.28 (0.14), residues: 1339 sheet: -0.93 (0.40), residues: 173 loop : -1.18 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 671 HIS 0.016 0.002 HIS C 412 PHE 0.023 0.002 PHE B 682 TYR 0.020 0.002 TYR A 732 ARG 0.015 0.001 ARG G 37 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 215 time to evaluate : 1.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 594 ARG cc_start: 0.9672 (mtm-85) cc_final: 0.9396 (mtp85) REVERT: A 674 MET cc_start: 0.5972 (mtm) cc_final: 0.5406 (mtt) REVERT: B 570 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8535 (mp0) REVERT: D 590 ASP cc_start: 0.8897 (t70) cc_final: 0.8606 (t0) REVERT: E 10 MET cc_start: 0.8532 (mmm) cc_final: 0.8157 (tpt) REVERT: E 176 TYR cc_start: 0.8920 (m-80) cc_final: 0.8442 (m-80) REVERT: F 192 MET cc_start: 0.8502 (mtt) cc_final: 0.8233 (mmp) REVERT: F 207 GLN cc_start: 0.9261 (tt0) cc_final: 0.8852 (tm-30) REVERT: G 9 GLN cc_start: 0.8363 (mp10) cc_final: 0.8141 (mp10) REVERT: G 99 ARG cc_start: 0.9246 (mtt-85) cc_final: 0.8761 (mtm-85) REVERT: H 24 MET cc_start: 0.9244 (tpt) cc_final: 0.9004 (tpp) REVERT: H 95 GLU cc_start: 0.9615 (tm-30) cc_final: 0.9301 (pm20) outliers start: 70 outliers final: 47 residues processed: 270 average time/residue: 0.3011 time to fit residues: 119.8229 Evaluate side-chains 247 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 199 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 546 PHE Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 126 GLU Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 158 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 8.9990 chunk 194 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 127 optimal weight: 7.9990 chunk 53 optimal weight: 0.5980 chunk 216 optimal weight: 0.9980 chunk 179 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 113 optimal weight: 20.0000 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN A 791 ASN B 569 ASN B 619 ASN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 17422 Z= 0.429 Angle : 0.694 11.932 23660 Z= 0.361 Chirality : 0.043 0.194 2745 Planarity : 0.004 0.045 2906 Dihedral : 4.264 29.632 2435 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.65 % Allowed : 19.22 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.19), residues: 2229 helix: 2.34 (0.14), residues: 1339 sheet: -1.05 (0.42), residues: 150 loop : -1.18 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 671 HIS 0.007 0.001 HIS C 412 PHE 0.025 0.002 PHE E 127 TYR 0.025 0.002 TYR D 424 ARG 0.006 0.001 ARG G 37 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 209 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 594 ARG cc_start: 0.9669 (mtm-85) cc_final: 0.9427 (mtp85) REVERT: A 674 MET cc_start: 0.5770 (mtm) cc_final: 0.5222 (mtt) REVERT: C 721 MET cc_start: 0.4347 (tpp) cc_final: 0.3840 (tpt) REVERT: D 590 ASP cc_start: 0.8900 (t70) cc_final: 0.8618 (t0) REVERT: E 10 MET cc_start: 0.8462 (mmm) cc_final: 0.8027 (tpt) REVERT: E 151 ILE cc_start: 0.9608 (OUTLIER) cc_final: 0.9326 (tt) REVERT: F 156 TYR cc_start: 0.9378 (t80) cc_final: 0.9073 (t80) REVERT: F 192 MET cc_start: 0.8468 (mtt) cc_final: 0.8187 (mmp) REVERT: F 207 GLN cc_start: 0.9262 (tt0) cc_final: 0.8859 (tm-30) REVERT: G 9 GLN cc_start: 0.8307 (mp10) cc_final: 0.8055 (mp10) REVERT: G 99 ARG cc_start: 0.9217 (mtt-85) cc_final: 0.8759 (mtm180) REVERT: H 95 GLU cc_start: 0.9645 (tm-30) cc_final: 0.9320 (pm20) outliers start: 61 outliers final: 49 residues processed: 257 average time/residue: 0.3010 time to fit residues: 113.3405 Evaluate side-chains 247 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 197 time to evaluate : 2.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 546 PHE Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 594 ARG Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 158 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 5.9990 chunk 24 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 182 optimal weight: 0.8980 chunk 121 optimal weight: 8.9990 chunk 215 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN B 569 ASN B 619 ASN B 747 ASN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 HIS H 205 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17422 Z= 0.200 Angle : 0.614 11.599 23660 Z= 0.315 Chirality : 0.041 0.221 2745 Planarity : 0.004 0.049 2906 Dihedral : 3.984 19.154 2435 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.87 % Allowed : 20.84 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.64 % 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: 1.84 (0.19), residues: 2229 helix: 2.66 (0.15), residues: 1342 sheet: -1.05 (0.43), residues: 152 loop : -1.10 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 671 HIS 0.007 0.001 HIS C 412 PHE 0.021 0.001 PHE B 682 TYR 0.025 0.001 TYR D 424 ARG 0.005 0.001 ARG D 586 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 235 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 594 ARG cc_start: 0.9644 (mtm-85) cc_final: 0.9422 (mtp85) REVERT: A 674 MET cc_start: 0.5630 (mtm) cc_final: 0.5068 (mtt) REVERT: B 408 MET cc_start: 0.7075 (tpt) cc_final: 0.6725 (tpt) REVERT: D 590 ASP cc_start: 0.8890 (t70) cc_final: 0.8620 (t0) REVERT: D 674 MET cc_start: 0.4908 (mmm) cc_final: 0.4537 (mmm) REVERT: E 10 MET cc_start: 0.8383 (mmm) cc_final: 0.8031 (tpt) REVERT: E 151 ILE cc_start: 0.9568 (OUTLIER) cc_final: 0.9327 (tt) REVERT: E 176 TYR cc_start: 0.8718 (m-80) cc_final: 0.8344 (m-80) REVERT: F 28 VAL cc_start: 0.9414 (OUTLIER) cc_final: 0.9212 (p) REVERT: F 192 MET cc_start: 0.8434 (mtt) cc_final: 0.8185 (mmp) REVERT: F 207 GLN cc_start: 0.9254 (tt0) cc_final: 0.8876 (tm-30) REVERT: G 9 GLN cc_start: 0.8190 (mp10) cc_final: 0.7941 (mp10) REVERT: G 99 ARG cc_start: 0.9204 (mtt-85) cc_final: 0.8716 (mtm180) REVERT: H 41 LYS cc_start: 0.9024 (tppt) cc_final: 0.8641 (tppt) REVERT: H 95 GLU cc_start: 0.9607 (tm-30) cc_final: 0.9253 (pm20) outliers start: 48 outliers final: 35 residues processed: 271 average time/residue: 0.2968 time to fit residues: 119.0795 Evaluate side-chains 249 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 212 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 546 PHE Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 594 ARG Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 126 GLU Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 150 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 0.9990 chunk 86 optimal weight: 0.0070 chunk 128 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 137 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 106 optimal weight: 30.0000 chunk 20 optimal weight: 2.9990 chunk 169 optimal weight: 0.3980 overall best weight: 1.4804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 569 ASN B 619 ASN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17422 Z= 0.231 Angle : 0.655 11.548 23660 Z= 0.331 Chirality : 0.041 0.235 2745 Planarity : 0.004 0.053 2906 Dihedral : 3.943 18.515 2434 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.05 % Allowed : 21.56 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.64 % 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: 1.85 (0.19), residues: 2229 helix: 2.61 (0.15), residues: 1348 sheet: -0.82 (0.45), residues: 144 loop : -1.06 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 671 HIS 0.007 0.001 HIS C 412 PHE 0.024 0.001 PHE B 682 TYR 0.029 0.001 TYR D 424 ARG 0.004 0.001 ARG B 586 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 219 time to evaluate : 1.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 594 ARG cc_start: 0.9638 (mtm-85) cc_final: 0.9416 (mtp85) REVERT: A 674 MET cc_start: 0.5585 (mtm) cc_final: 0.5014 (mtt) REVERT: B 408 MET cc_start: 0.7176 (tpt) cc_final: 0.6768 (tpt) REVERT: B 493 LYS cc_start: 0.6491 (mmtt) cc_final: 0.5209 (tppt) REVERT: D 590 ASP cc_start: 0.8875 (t70) cc_final: 0.8619 (t0) REVERT: D 674 MET cc_start: 0.4982 (mmm) cc_final: 0.4607 (mmm) REVERT: E 10 MET cc_start: 0.8394 (mmm) cc_final: 0.8030 (tpt) REVERT: E 151 ILE cc_start: 0.9549 (OUTLIER) cc_final: 0.9281 (tt) REVERT: F 28 VAL cc_start: 0.9455 (OUTLIER) cc_final: 0.9237 (p) REVERT: F 192 MET cc_start: 0.8434 (mtt) cc_final: 0.8162 (mmp) REVERT: F 207 GLN cc_start: 0.9254 (tt0) cc_final: 0.8870 (tm-30) REVERT: G 9 GLN cc_start: 0.8186 (mp10) cc_final: 0.7937 (mp10) REVERT: G 99 ARG cc_start: 0.9178 (mtt-85) cc_final: 0.8676 (mtm-85) REVERT: H 95 GLU cc_start: 0.9606 (tm-30) cc_final: 0.9266 (pm20) outliers start: 51 outliers final: 40 residues processed: 256 average time/residue: 0.3020 time to fit residues: 114.4747 Evaluate side-chains 258 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 216 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 546 PHE Chi-restraints excluded: chain B residue 594 ARG Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain D residue 424 TYR Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 150 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 5.9990 chunk 206 optimal weight: 0.7980 chunk 188 optimal weight: 0.8980 chunk 201 optimal weight: 1.9990 chunk 121 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 157 optimal weight: 5.9990 chunk 61 optimal weight: 20.0000 chunk 181 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 200 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 619 ASN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 GLN F 82 HIS ** H 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 ASN H 205 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.5094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17422 Z= 0.234 Angle : 0.651 12.856 23660 Z= 0.330 Chirality : 0.041 0.251 2745 Planarity : 0.004 0.056 2906 Dihedral : 3.914 21.139 2434 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.99 % Allowed : 21.98 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.64 % 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: 1.93 (0.19), residues: 2229 helix: 2.64 (0.15), residues: 1346 sheet: -0.76 (0.43), residues: 157 loop : -0.94 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 671 HIS 0.007 0.001 HIS C 412 PHE 0.020 0.001 PHE B 682 TYR 0.025 0.001 TYR D 424 ARG 0.004 0.001 ARG D 586 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 219 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 594 ARG cc_start: 0.9637 (mtm-85) cc_final: 0.9418 (mtp85) REVERT: B 408 MET cc_start: 0.7083 (tpt) cc_final: 0.6798 (tpt) REVERT: C 670 MET cc_start: 0.5820 (mmm) cc_final: 0.5514 (mmm) REVERT: D 590 ASP cc_start: 0.8860 (t70) cc_final: 0.8611 (t0) REVERT: D 674 MET cc_start: 0.4877 (mmm) cc_final: 0.4516 (mmm) REVERT: E 10 MET cc_start: 0.8396 (mmm) cc_final: 0.8025 (tpt) REVERT: E 151 ILE cc_start: 0.9541 (OUTLIER) cc_final: 0.9268 (tt) REVERT: F 192 MET cc_start: 0.8438 (mtt) cc_final: 0.8162 (mmp) REVERT: F 207 GLN cc_start: 0.9257 (tt0) cc_final: 0.8871 (tm-30) REVERT: G 99 ARG cc_start: 0.9184 (mtt-85) cc_final: 0.8677 (mtm180) REVERT: H 95 GLU cc_start: 0.9606 (tm-30) cc_final: 0.9265 (pm20) outliers start: 50 outliers final: 41 residues processed: 255 average time/residue: 0.3193 time to fit residues: 121.3531 Evaluate side-chains 255 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 213 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 546 PHE Chi-restraints excluded: chain B residue 594 ARG Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 150 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 0.9990 chunk 212 optimal weight: 5.9990 chunk 129 optimal weight: 0.0870 chunk 100 optimal weight: 20.0000 chunk 147 optimal weight: 8.9990 chunk 223 optimal weight: 0.8980 chunk 205 optimal weight: 0.8980 chunk 177 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 108 optimal weight: 6.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 619 ASN C 412 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.5203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17422 Z= 0.176 Angle : 0.652 13.503 23660 Z= 0.328 Chirality : 0.040 0.252 2745 Planarity : 0.004 0.060 2906 Dihedral : 3.881 18.060 2434 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.63 % Allowed : 22.63 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.19), residues: 2229 helix: 2.72 (0.15), residues: 1348 sheet: -0.64 (0.43), residues: 157 loop : -0.83 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 671 HIS 0.008 0.001 HIS C 412 PHE 0.015 0.001 PHE B 682 TYR 0.020 0.001 TYR D 424 ARG 0.006 0.001 ARG H 6 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 226 time to evaluate : 1.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.5129 (mmm) cc_final: 0.4864 (mmm) REVERT: A 594 ARG cc_start: 0.9621 (mtm-85) cc_final: 0.9416 (mtp85) REVERT: B 408 MET cc_start: 0.6886 (tpt) cc_final: 0.6628 (tpt) REVERT: C 587 GLN cc_start: 0.8863 (tp-100) cc_final: 0.8523 (tp-100) REVERT: C 670 MET cc_start: 0.5663 (mmm) cc_final: 0.5402 (mmm) REVERT: D 524 GLU cc_start: 0.8874 (mp0) cc_final: 0.8645 (mp0) REVERT: D 590 ASP cc_start: 0.8848 (t70) cc_final: 0.8609 (t0) REVERT: D 674 MET cc_start: 0.4825 (mmm) cc_final: 0.4506 (mmm) REVERT: E 10 MET cc_start: 0.8397 (mmm) cc_final: 0.8033 (tpt) REVERT: E 128 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.8111 (m-80) REVERT: E 151 ILE cc_start: 0.9530 (OUTLIER) cc_final: 0.9278 (tt) REVERT: E 176 TYR cc_start: 0.8669 (m-80) cc_final: 0.8222 (m-80) REVERT: F 185 LEU cc_start: 0.9047 (tp) cc_final: 0.8835 (tp) REVERT: F 192 MET cc_start: 0.8446 (mtt) cc_final: 0.8124 (mmp) REVERT: F 207 GLN cc_start: 0.9148 (tt0) cc_final: 0.8752 (tm-30) REVERT: G 99 ARG cc_start: 0.9177 (mtt-85) cc_final: 0.8669 (mtm180) REVERT: G 110 LEU cc_start: 0.9494 (tp) cc_final: 0.9207 (tp) REVERT: H 24 MET cc_start: 0.9307 (tpt) cc_final: 0.9058 (tpp) REVERT: H 95 GLU cc_start: 0.9604 (tm-30) cc_final: 0.9269 (pm20) outliers start: 44 outliers final: 35 residues processed: 256 average time/residue: 0.3056 time to fit residues: 116.5325 Evaluate side-chains 256 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 219 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 546 PHE Chi-restraints excluded: chain B residue 594 ARG Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 128 TYR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 126 GLU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 73 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.77 > 50: distance: 32 - 58: 10.979 distance: 39 - 63: 11.115 distance: 43 - 69: 27.307 distance: 52 - 58: 10.909 distance: 58 - 59: 36.063 distance: 59 - 60: 34.804 distance: 59 - 62: 47.341 distance: 60 - 61: 28.518 distance: 60 - 63: 10.909 distance: 63 - 64: 41.673 distance: 64 - 65: 40.227 distance: 65 - 66: 30.947 distance: 65 - 69: 30.403 distance: 67 - 68: 55.179 distance: 69 - 70: 55.801 distance: 70 - 71: 25.248 distance: 70 - 73: 48.938 distance: 71 - 72: 19.532 distance: 71 - 74: 29.133 distance: 74 - 75: 5.137 distance: 75 - 76: 13.954 distance: 75 - 78: 37.145 distance: 76 - 77: 50.087 distance: 76 - 79: 34.177 distance: 79 - 80: 24.264 distance: 79 - 85: 11.366 distance: 80 - 81: 14.914 distance: 80 - 83: 16.736 distance: 81 - 82: 41.084 distance: 81 - 86: 18.563 distance: 83 - 84: 21.454 distance: 84 - 85: 14.358 distance: 86 - 87: 17.431 distance: 87 - 88: 14.635 distance: 87 - 90: 26.317 distance: 88 - 89: 18.163 distance: 88 - 92: 12.283 distance: 90 - 91: 14.931 distance: 92 - 93: 10.717 distance: 93 - 94: 8.904 distance: 93 - 96: 18.889 distance: 94 - 95: 8.621 distance: 94 - 99: 6.055 distance: 96 - 97: 25.661 distance: 96 - 98: 20.185 distance: 99 - 100: 33.982 distance: 100 - 101: 16.367 distance: 100 - 103: 20.905 distance: 101 - 102: 52.157 distance: 101 - 110: 31.684 distance: 103 - 104: 9.592 distance: 104 - 105: 15.690 distance: 104 - 106: 7.698 distance: 105 - 107: 8.008 distance: 106 - 108: 8.698 distance: 107 - 109: 6.631 distance: 108 - 109: 8.738 distance: 110 - 111: 37.898 distance: 111 - 112: 18.598 distance: 111 - 114: 40.075 distance: 112 - 113: 27.510 distance: 112 - 117: 38.598 distance: 114 - 115: 45.210 distance: 114 - 116: 45.796 distance: 117 - 118: 13.898 distance: 118 - 119: 14.087 distance: 118 - 121: 25.300 distance: 119 - 120: 42.083 distance: 119 - 128: 14.476 distance: 121 - 122: 43.214 distance: 122 - 123: 21.940 distance: 123 - 124: 10.767 distance: 125 - 126: 11.695 distance: 125 - 127: 6.020