Starting phenix.real_space_refine on Tue Apr 9 18:04:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3x_17398/04_2024/8p3x_17398.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3x_17398/04_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_17398/04_2024/8p3x_17398.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3x_17398/04_2024/8p3x_17398.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3x_17398/04_2024/8p3x_17398.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3x_17398/04_2024/8p3x_17398.pdb" } 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 11.90, per 1000 atoms: 0.70 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: 7.17 Conformation dependent library (CDL) restraints added in 4.5 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: 1.83 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: 5.78 Time building geometry restraints manager: 7.74 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 2.440 nonbonded pdb=" O SER E 104 " pdb=" N ILE E 106 " model vdw 2.250 2.520 nonbonded pdb=" N VAL D 395 " pdb=" O LYS D 439 " model vdw 2.261 2.520 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 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.500 Check model and map are aligned: 0.250 Set scattering table: 0.180 Process input model: 52.550 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.090 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.650 ------------------------------------------------------------------------------- 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 : 1.912 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: 0.3702 time to fit residues: 219.7849 Evaluate side-chains 246 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 238 time to evaluate : 2.027 ------------------------------------------------------------------------------- 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: 0.6980 chunk 169 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 175 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 130 optimal weight: 0.6980 chunk 203 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.3032 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= 0.189 Angle : 0.604 11.625 23660 Z= 0.322 Chirality : 0.042 0.272 2745 Planarity : 0.004 0.040 2906 Dihedral : 4.653 59.178 2451 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.10 % Allowed : 15.09 % Favored : 82.81 % 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: 0.96 (0.18), residues: 2229 helix: 2.04 (0.14), residues: 1322 sheet: -1.38 (0.37), residues: 159 loop : -1.54 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 671 HIS 0.006 0.001 HIS D 435 PHE 0.013 0.001 PHE D 623 TYR 0.015 0.001 TYR D 469 ARG 0.007 0.001 ARG D 586 *********************** 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: 35 poor density : 291 time to evaluate : 2.113 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: symmetry clash revert: symmetry clash REVERT: A 590 ASP cc_start: 0.8771 (p0) cc_final: 0.8428 (p0) REVERT: A 591 ILE cc_start: 0.9141 (tp) cc_final: 0.8905 (pt) REVERT: A 594 ARG cc_start: 0.9617 (mtm-85) cc_final: 0.9321 (mtp85) REVERT: A 674 MET cc_start: 0.5753 (mtm) cc_final: 0.5200 (mtt) REVERT: C 587 GLN cc_start: 0.8955 (mm-40) cc_final: 0.8600 (tp-100) REVERT: D 519 ASP cc_start: 0.9244 (m-30) cc_final: 0.9010 (m-30) REVERT: D 524 GLU cc_start: 0.9135 (mp0) cc_final: 0.8829 (mp0) REVERT: D 590 ASP cc_start: 0.8914 (t70) cc_final: 0.8644 (t0) REVERT: E 56 GLU cc_start: 0.8880 (pt0) cc_final: 0.8392 (pp20) REVERT: E 70 GLU cc_start: 0.8231 (pp20) cc_final: 0.7986 (pp20) REVERT: E 78 LYS cc_start: 0.9119 (pttt) cc_final: 0.8903 (pttm) REVERT: E 81 ASP cc_start: 0.9224 (t0) cc_final: 0.8958 (p0) REVERT: E 176 TYR cc_start: 0.8433 (m-80) cc_final: 0.7754 (m-80) REVERT: E 195 VAL cc_start: 0.9041 (OUTLIER) cc_final: 0.8797 (t) REVERT: F 10 MET cc_start: 0.8725 (mmm) cc_final: 0.8062 (tpp) REVERT: F 58 MET cc_start: 0.9366 (tpp) cc_final: 0.9086 (mmp) REVERT: F 160 ASN cc_start: 0.8678 (m-40) cc_final: 0.8454 (m110) REVERT: F 174 TYR cc_start: 0.8427 (p90) cc_final: 0.7452 (p90) REVERT: F 192 MET cc_start: 0.8466 (mtt) cc_final: 0.8206 (mmp) REVERT: F 207 GLN cc_start: 0.9293 (tt0) cc_final: 0.8787 (tm-30) REVERT: G 6 ARG cc_start: 0.8002 (tpt170) cc_final: 0.7261 (tpt170) REVERT: G 24 MET cc_start: 0.9088 (tpt) cc_final: 0.8347 (tpt) REVERT: G 99 ARG cc_start: 0.9165 (mtt-85) cc_final: 0.8690 (mtm180) REVERT: H 31 ASP cc_start: 0.8640 (m-30) cc_final: 0.8413 (m-30) REVERT: H 95 GLU cc_start: 0.9524 (tm-30) cc_final: 0.9244 (pm20) outliers start: 35 outliers final: 16 residues processed: 311 average time/residue: 0.3312 time to fit residues: 149.9460 Evaluate side-chains 249 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 232 time to evaluate : 1.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain E residue 59 THR 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 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: 0.9980 chunk 169 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 220 optimal weight: 0.9980 chunk 181 optimal weight: 2.9990 chunk 202 optimal weight: 0.6980 chunk 69 optimal weight: 20.0000 chunk 163 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 ASN ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 ASN B 619 ASN ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN E 9 GLN E 72 ASN F 149 ASN F 205 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17422 Z= 0.231 Angle : 0.571 12.311 23660 Z= 0.302 Chirality : 0.040 0.211 2745 Planarity : 0.004 0.039 2906 Dihedral : 3.983 56.926 2435 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.87 % Allowed : 16.95 % Favored : 80.18 % 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: 1.72 (0.19), residues: 2229 helix: 2.63 (0.15), residues: 1328 sheet: -0.98 (0.40), residues: 161 loop : -1.23 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 671 HIS 0.007 0.001 HIS E 82 PHE 0.011 0.001 PHE G 107 TYR 0.014 0.001 TYR D 732 ARG 0.006 0.001 ARG D 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 293 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 245 time to evaluate : 1.908 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 594 ARG cc_start: 0.9637 (mtm-85) cc_final: 0.9353 (mtp85) REVERT: A 674 MET cc_start: 0.5748 (mtm) cc_final: 0.5196 (mtt) REVERT: B 670 MET cc_start: 0.6617 (mmm) cc_final: 0.6332 (mmm) REVERT: D 519 ASP cc_start: 0.9312 (m-30) cc_final: 0.9007 (m-30) REVERT: D 590 ASP cc_start: 0.8897 (t70) cc_final: 0.8620 (t0) REVERT: E 10 MET cc_start: 0.8653 (mmm) cc_final: 0.8351 (tpp) REVERT: E 56 GLU cc_start: 0.8842 (pt0) cc_final: 0.8414 (pp20) REVERT: E 70 GLU cc_start: 0.8556 (pp20) cc_final: 0.8345 (pp20) REVERT: E 78 LYS cc_start: 0.9128 (pttt) cc_final: 0.8903 (pttm) REVERT: F 81 ASP cc_start: 0.9417 (t0) cc_final: 0.9216 (t0) REVERT: F 110 LEU cc_start: 0.8925 (tp) cc_final: 0.8632 (tp) REVERT: F 160 ASN cc_start: 0.8650 (m-40) cc_final: 0.8393 (m110) REVERT: F 192 MET cc_start: 0.8547 (mtt) cc_final: 0.8251 (mmp) REVERT: F 207 GLN cc_start: 0.9143 (tt0) cc_final: 0.8715 (tm-30) REVERT: G 10 MET cc_start: 0.9070 (mmm) cc_final: 0.8724 (tpp) REVERT: G 99 ARG cc_start: 0.9182 (mtt-85) cc_final: 0.8670 (mtt180) REVERT: H 31 ASP cc_start: 0.8656 (m-30) cc_final: 0.8394 (m-30) REVERT: H 95 GLU cc_start: 0.9567 (tm-30) cc_final: 0.9238 (pm20) outliers start: 48 outliers final: 25 residues processed: 281 average time/residue: 0.3414 time to fit residues: 141.7126 Evaluate side-chains 245 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 220 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 590 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 59 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 40 CYS 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 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 57 VAL Chi-restraints excluded: chain H residue 61 SER 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: 3.9990 chunk 153 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 22 optimal weight: 30.0000 chunk 97 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 204 optimal weight: 0.9980 chunk 216 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 193 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN F 82 HIS F 205 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.3911 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= 0.209 Angle : 0.566 11.233 23660 Z= 0.299 Chirality : 0.040 0.166 2745 Planarity : 0.003 0.041 2906 Dihedral : 3.868 49.006 2435 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.05 % Allowed : 17.96 % Favored : 78.98 % 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: 1.87 (0.19), residues: 2229 helix: 2.67 (0.15), residues: 1344 sheet: -0.73 (0.42), residues: 161 loop : -1.16 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP D 671 HIS 0.010 0.001 HIS C 412 PHE 0.010 0.001 PHE G 73 TYR 0.028 0.001 TYR A 732 ARG 0.006 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 291 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 240 time to evaluate : 1.823 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: 0.9630 (mtm-85) cc_final: 0.9353 (mtp85) REVERT: A 674 MET cc_start: 0.5944 (mtm) cc_final: 0.5377 (mtt) REVERT: D 590 ASP cc_start: 0.8893 (t70) cc_final: 0.8613 (t0) REVERT: D 721 MET cc_start: 0.5754 (ppp) cc_final: 0.5372 (ppp) REVERT: E 56 GLU cc_start: 0.8851 (pt0) cc_final: 0.8541 (pp20) REVERT: E 70 GLU cc_start: 0.8711 (pp20) cc_final: 0.8488 (pp20) REVERT: E 78 LYS cc_start: 0.9045 (pttt) cc_final: 0.8843 (pttm) REVERT: F 110 LEU cc_start: 0.8950 (tp) cc_final: 0.8631 (tp) REVERT: F 160 ASN cc_start: 0.8655 (m-40) cc_final: 0.8366 (m110) REVERT: F 192 MET cc_start: 0.8463 (mtt) cc_final: 0.8211 (mmp) REVERT: F 207 GLN cc_start: 0.9139 (tt0) cc_final: 0.8727 (tm-30) REVERT: G 10 MET cc_start: 0.9030 (mmm) cc_final: 0.8477 (tpp) REVERT: G 14 THR cc_start: 0.9490 (t) cc_final: 0.9221 (p) REVERT: G 99 ARG cc_start: 0.9167 (mtt-85) cc_final: 0.8656 (mtm180) REVERT: H 95 GLU cc_start: 0.9561 (tm-30) cc_final: 0.9223 (pm20) outliers start: 51 outliers final: 33 residues processed: 280 average time/residue: 0.3350 time to fit residues: 137.2310 Evaluate side-chains 249 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 216 time to evaluate : 1.958 ------------------------------------------------------------------------------- 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 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 C residue 412 HIS Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 590 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 160 ASN 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 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 57 VAL Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 158 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 161 optimal weight: 0.2980 chunk 89 optimal weight: 9.9990 chunk 184 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 110 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 54 optimal weight: 0.0070 overall best weight: 1.8604 ------------------------------------------------------------------------------- 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 587 GLN B 619 ASN ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 791 ASN F 205 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17422 Z= 0.257 Angle : 0.590 11.263 23660 Z= 0.307 Chirality : 0.040 0.202 2745 Planarity : 0.004 0.041 2906 Dihedral : 3.848 37.958 2435 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.59 % Allowed : 18.50 % Favored : 77.90 % 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: 1.96 (0.19), residues: 2229 helix: 2.70 (0.15), residues: 1349 sheet: -0.46 (0.42), residues: 171 loop : -1.11 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP D 671 HIS 0.021 0.002 HIS C 412 PHE 0.024 0.001 PHE B 682 TYR 0.021 0.001 TYR F 174 ARG 0.005 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 292 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 232 time to evaluate : 2.016 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: 0.9644 (mtm-85) cc_final: 0.9398 (mtp85) REVERT: A 674 MET cc_start: 0.5874 (mtm) cc_final: 0.5307 (mtt) REVERT: B 755 GLU cc_start: 0.3954 (tp30) cc_final: 0.3628 (tp30) REVERT: D 590 ASP cc_start: 0.8883 (t70) cc_final: 0.8611 (t0) REVERT: E 10 MET cc_start: 0.8529 (mmm) cc_final: 0.8147 (tpt) REVERT: F 110 LEU cc_start: 0.9014 (tp) cc_final: 0.8653 (tp) REVERT: F 192 MET cc_start: 0.8501 (mtt) cc_final: 0.8257 (mmp) REVERT: F 207 GLN cc_start: 0.9243 (tt0) cc_final: 0.8831 (tm-30) REVERT: G 10 MET cc_start: 0.9013 (mmm) cc_final: 0.8411 (tpp) REVERT: G 14 THR cc_start: 0.9497 (t) cc_final: 0.9250 (p) REVERT: G 24 MET cc_start: 0.9011 (tpt) cc_final: 0.8773 (mmm) REVERT: G 99 ARG cc_start: 0.9203 (mtt-85) cc_final: 0.8728 (mtm180) REVERT: H 95 GLU cc_start: 0.9587 (tm-30) cc_final: 0.9253 (pm20) outliers start: 60 outliers final: 41 residues processed: 277 average time/residue: 0.3145 time to fit residues: 128.5772 Evaluate side-chains 251 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 210 time to evaluate : 1.996 ------------------------------------------------------------------------------- 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 454 ASP 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 C residue 464 VAL Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 26 ILE 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 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 57 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 61 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 30.0000 chunk 194 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 216 optimal weight: 0.9980 chunk 179 optimal weight: 20.0000 chunk 100 optimal weight: 20.0000 chunk 18 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 113 optimal weight: 8.9990 overall best weight: 3.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN B 619 ASN C 412 HIS ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN H 205 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 17422 Z= 0.461 Angle : 0.707 11.354 23660 Z= 0.368 Chirality : 0.043 0.217 2745 Planarity : 0.004 0.046 2906 Dihedral : 4.172 29.771 2435 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.65 % Allowed : 18.92 % Favored : 77.43 % 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: 1.64 (0.19), residues: 2229 helix: 2.36 (0.14), residues: 1351 sheet: -0.56 (0.43), residues: 166 loop : -1.08 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 671 HIS 0.007 0.002 HIS F 82 PHE 0.030 0.002 PHE G 73 TYR 0.019 0.002 TYR C 523 ARG 0.004 0.001 ARG D 586 *********************** 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 269 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 208 time to evaluate : 1.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 594 ARG cc_start: 0.9660 (mtm-85) cc_final: 0.9425 (mtp85) REVERT: A 674 MET cc_start: 0.6014 (mtm) cc_final: 0.5486 (mtt) REVERT: B 755 GLU cc_start: 0.4423 (tp30) cc_final: 0.4209 (tp30) REVERT: D 590 ASP cc_start: 0.8911 (t70) cc_final: 0.8621 (t0) REVERT: D 721 MET cc_start: 0.6266 (ppp) cc_final: 0.5559 (ppp) REVERT: E 10 MET cc_start: 0.8421 (mmm) cc_final: 0.8005 (tpt) REVERT: E 37 ARG cc_start: 0.9314 (tmm-80) cc_final: 0.9039 (tpt-90) REVERT: E 56 GLU cc_start: 0.9136 (mp0) cc_final: 0.8666 (tt0) REVERT: E 176 TYR cc_start: 0.8885 (m-80) cc_final: 0.8433 (m-80) REVERT: F 192 MET cc_start: 0.8493 (mtt) cc_final: 0.8222 (mmp) REVERT: F 207 GLN cc_start: 0.9255 (tt0) cc_final: 0.8849 (tm-30) REVERT: G 10 MET cc_start: 0.9015 (mmm) cc_final: 0.8631 (tpp) REVERT: G 99 ARG cc_start: 0.9226 (mtt-85) cc_final: 0.8742 (mtm-85) REVERT: H 95 GLU cc_start: 0.9623 (tm-30) cc_final: 0.9281 (pm20) outliers start: 61 outliers final: 48 residues processed: 255 average time/residue: 0.3267 time to fit residues: 121.6376 Evaluate side-chains 246 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 198 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 546 PHE 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 B residue 673 TYR Chi-restraints excluded: chain B residue 807 MET 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 C residue 590 ASP Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 160 ASN 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 57 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 H residue 8 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 57 VAL 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: 4.9990 chunk 24 optimal weight: 20.0000 chunk 123 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 182 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 619 ASN ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 747 ASN E 160 ASN F 205 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.4744 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= 0.196 Angle : 0.603 11.790 23660 Z= 0.308 Chirality : 0.040 0.216 2745 Planarity : 0.004 0.051 2906 Dihedral : 3.889 17.883 2434 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.87 % Allowed : 20.36 % Favored : 76.77 % 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: 1.97 (0.19), residues: 2229 helix: 2.68 (0.15), residues: 1348 sheet: -0.73 (0.42), residues: 164 loop : -0.95 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D 671 HIS 0.005 0.001 HIS C 412 PHE 0.026 0.001 PHE G 73 TYR 0.021 0.001 TYR F 156 ARG 0.004 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 281 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 233 time to evaluate : 2.209 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: 0.9628 (mtm-85) cc_final: 0.9420 (mtp85) REVERT: A 674 MET cc_start: 0.5627 (mtm) cc_final: 0.5058 (mtt) REVERT: B 668 ASP cc_start: 0.6819 (p0) cc_final: 0.6473 (m-30) REVERT: B 755 GLU cc_start: 0.4360 (tp30) cc_final: 0.4048 (tp30) REVERT: C 721 MET cc_start: 0.4084 (tpp) cc_final: 0.3877 (tpt) REVERT: D 590 ASP cc_start: 0.8883 (t70) cc_final: 0.8609 (t0) REVERT: D 721 MET cc_start: 0.6545 (ppp) cc_final: 0.5798 (ppp) REVERT: E 10 MET cc_start: 0.8327 (mmm) cc_final: 0.7910 (tpt) REVERT: F 110 LEU cc_start: 0.9002 (tp) cc_final: 0.8598 (tp) REVERT: F 192 MET cc_start: 0.8448 (mtt) cc_final: 0.8183 (mmp) REVERT: F 207 GLN cc_start: 0.9250 (tt0) cc_final: 0.8871 (tm-30) REVERT: G 10 MET cc_start: 0.8917 (mmm) cc_final: 0.8502 (tpp) REVERT: G 99 ARG cc_start: 0.9194 (mtt-85) cc_final: 0.8695 (mtm-85) REVERT: H 95 GLU cc_start: 0.9607 (tm-30) cc_final: 0.9247 (pm20) outliers start: 48 outliers final: 37 residues processed: 265 average time/residue: 0.3148 time to fit residues: 123.1418 Evaluate side-chains 252 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 215 time to evaluate : 2.104 ------------------------------------------------------------------------------- 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 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 613 ILE Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 673 TYR 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 C residue 590 ASP Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 149 ASN 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 195 VAL Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 42 THR 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 150 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 65 optimal weight: 20.0000 chunk 42 optimal weight: 0.7980 chunk 41 optimal weight: 10.0000 chunk 137 optimal weight: 0.6980 chunk 147 optimal weight: 6.9990 chunk 106 optimal weight: 30.0000 chunk 20 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN B 619 ASN ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 747 ASN F 205 HIS H 205 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 17422 Z= 0.305 Angle : 0.656 12.270 23660 Z= 0.335 Chirality : 0.041 0.226 2745 Planarity : 0.004 0.056 2906 Dihedral : 3.907 18.379 2434 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.10 % Favored : 96.85 % Rotamer: Outliers : 3.23 % Allowed : 20.60 % Favored : 76.17 % 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: 1.89 (0.19), residues: 2229 helix: 2.60 (0.15), residues: 1347 sheet: -0.75 (0.43), residues: 166 loop : -0.94 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP D 671 HIS 0.006 0.001 HIS E 132 PHE 0.026 0.002 PHE B 682 TYR 0.017 0.001 TYR F 156 ARG 0.005 0.001 ARG E 37 *********************** 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 273 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 219 time to evaluate : 2.015 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: 0.9636 (mtm-85) cc_final: 0.9418 (mtp85) REVERT: A 674 MET cc_start: 0.5661 (mtm) cc_final: 0.5093 (mtt) REVERT: B 755 GLU cc_start: 0.4694 (tp30) cc_final: 0.4374 (tp30) REVERT: D 590 ASP cc_start: 0.8894 (t70) cc_final: 0.8628 (t0) REVERT: D 721 MET cc_start: 0.6351 (ppp) cc_final: 0.5533 (ppp) REVERT: E 10 MET cc_start: 0.8349 (mmm) cc_final: 0.7924 (tpt) REVERT: E 56 GLU cc_start: 0.9268 (mp0) cc_final: 0.8745 (tt0) REVERT: E 117 MET cc_start: 0.9008 (mmm) cc_final: 0.8730 (mtm) REVERT: E 128 TYR cc_start: 0.8829 (OUTLIER) cc_final: 0.8160 (m-80) REVERT: F 192 MET cc_start: 0.8445 (mtt) cc_final: 0.8170 (mmp) REVERT: F 207 GLN cc_start: 0.9255 (tt0) cc_final: 0.8872 (tm-30) REVERT: G 10 MET cc_start: 0.8904 (mmm) cc_final: 0.8512 (tpp) REVERT: G 99 ARG cc_start: 0.9178 (mtt-85) cc_final: 0.8688 (mtm-85) REVERT: H 6 ARG cc_start: 0.9034 (ptm-80) cc_final: 0.8810 (ttp80) REVERT: H 95 GLU cc_start: 0.9607 (tm-30) cc_final: 0.9248 (pm20) outliers start: 54 outliers final: 46 residues processed: 256 average time/residue: 0.3144 time to fit residues: 119.0063 Evaluate side-chains 262 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 215 time to evaluate : 1.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 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 B residue 673 TYR 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 590 ASP Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 128 TYR Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 30 THR 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 57 VAL Chi-restraints excluded: chain G residue 73 PHE 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 42 THR 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: 10.0000 chunk 206 optimal weight: 2.9990 chunk 188 optimal weight: 0.7980 chunk 201 optimal weight: 0.7980 chunk 121 optimal weight: 20.0000 chunk 87 optimal weight: 8.9990 chunk 157 optimal weight: 5.9990 chunk 61 optimal weight: 30.0000 chunk 181 optimal weight: 0.9990 chunk 190 optimal weight: 0.9980 chunk 200 optimal weight: 8.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN B 619 ASN ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 747 ASN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17422 Z= 0.210 Angle : 0.624 12.539 23660 Z= 0.315 Chirality : 0.040 0.234 2745 Planarity : 0.004 0.060 2906 Dihedral : 3.810 19.192 2434 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.81 % Allowed : 20.96 % Favored : 76.23 % 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: 2.00 (0.19), residues: 2229 helix: 2.69 (0.15), residues: 1350 sheet: -0.71 (0.43), residues: 164 loop : -0.93 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP D 671 HIS 0.006 0.001 HIS C 412 PHE 0.025 0.001 PHE B 515 TYR 0.017 0.001 TYR F 156 ARG 0.010 0.001 ARG A 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 268 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 221 time to evaluate : 2.053 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: 0.9621 (mtm-85) cc_final: 0.9414 (mtp85) REVERT: B 755 GLU cc_start: 0.5504 (tp30) cc_final: 0.5253 (tp30) REVERT: C 721 MET cc_start: 0.4146 (tpp) cc_final: 0.3913 (tpt) REVERT: D 590 ASP cc_start: 0.8838 (t70) cc_final: 0.8614 (t0) REVERT: D 721 MET cc_start: 0.6373 (ppp) cc_final: 0.5443 (ppp) REVERT: E 10 MET cc_start: 0.8330 (mmm) cc_final: 0.7902 (tpt) REVERT: E 56 GLU cc_start: 0.9226 (mp0) cc_final: 0.8699 (tt0) REVERT: E 128 TYR cc_start: 0.8821 (OUTLIER) cc_final: 0.8141 (m-80) REVERT: F 192 MET cc_start: 0.8451 (mtt) cc_final: 0.8169 (mmp) REVERT: F 207 GLN cc_start: 0.9253 (tt0) cc_final: 0.8869 (tm-30) REVERT: G 10 MET cc_start: 0.8841 (mmm) cc_final: 0.8426 (tpp) REVERT: G 99 ARG cc_start: 0.9171 (mtt-85) cc_final: 0.8649 (mtm-85) REVERT: H 6 ARG cc_start: 0.9056 (ptm-80) cc_final: 0.8728 (ttp80) REVERT: H 95 GLU cc_start: 0.9611 (tm-30) cc_final: 0.9246 (pm20) outliers start: 47 outliers final: 39 residues processed: 252 average time/residue: 0.3171 time to fit residues: 118.2965 Evaluate side-chains 255 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 215 time to evaluate : 2.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 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 594 ARG Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 673 TYR 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 590 ASP Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 128 TYR Chi-restraints excluded: chain E residue 149 ASN 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 155 VAL Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 135 ILE 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 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: 0.7980 chunk 212 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 100 optimal weight: 0.0470 chunk 147 optimal weight: 4.9990 chunk 223 optimal weight: 2.9990 chunk 205 optimal weight: 0.8980 chunk 177 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 overall best weight: 1.1480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN B 619 ASN ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17422 Z= 0.201 Angle : 0.632 13.337 23660 Z= 0.317 Chirality : 0.040 0.240 2745 Planarity : 0.004 0.065 2906 Dihedral : 3.778 20.126 2434 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.87 % Allowed : 21.08 % Favored : 76.05 % 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: 2.07 (0.19), residues: 2229 helix: 2.74 (0.15), residues: 1350 sheet: -0.62 (0.44), residues: 159 loop : -0.91 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP D 671 HIS 0.006 0.001 HIS C 412 PHE 0.028 0.001 PHE B 515 TYR 0.016 0.001 TYR F 156 ARG 0.009 0.001 ARG G 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 269 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 221 time to evaluate : 2.118 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: 0.9620 (mtm-85) cc_final: 0.9415 (mtp85) REVERT: D 590 ASP cc_start: 0.8831 (t70) cc_final: 0.8618 (t0) REVERT: D 721 MET cc_start: 0.6403 (ppp) cc_final: 0.5398 (ppp) REVERT: E 10 MET cc_start: 0.8333 (mmm) cc_final: 0.7906 (tpt) REVERT: E 56 GLU cc_start: 0.9310 (mp0) cc_final: 0.8766 (tt0) REVERT: E 128 TYR cc_start: 0.8818 (OUTLIER) cc_final: 0.8140 (m-80) REVERT: F 10 MET cc_start: 0.9016 (mmm) cc_final: 0.8570 (mmm) REVERT: F 13 THR cc_start: 0.9259 (m) cc_final: 0.9009 (t) REVERT: F 192 MET cc_start: 0.8452 (mtt) cc_final: 0.8164 (mmp) REVERT: F 207 GLN cc_start: 0.9252 (tt0) cc_final: 0.8866 (tm-30) REVERT: G 10 MET cc_start: 0.8833 (mmm) cc_final: 0.8436 (tpp) REVERT: G 24 MET cc_start: 0.8918 (tpt) cc_final: 0.8523 (tpp) REVERT: G 99 ARG cc_start: 0.9170 (mtt-85) cc_final: 0.8652 (mtm-85) REVERT: G 206 LYS cc_start: 0.9659 (ttpt) cc_final: 0.9448 (tptt) REVERT: H 6 ARG cc_start: 0.9078 (ptm-80) cc_final: 0.8756 (ttp80) REVERT: H 95 GLU cc_start: 0.9608 (tm-30) cc_final: 0.9252 (pm20) REVERT: H 200 MET cc_start: 0.8697 (ttp) cc_final: 0.8282 (tpt) outliers start: 48 outliers final: 40 residues processed: 253 average time/residue: 0.3240 time to fit residues: 121.5560 Evaluate side-chains 258 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 217 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 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 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 590 ASP Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 506 LYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 128 TYR Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 30 THR 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 57 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 135 ILE 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 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 141 optimal weight: 8.9990 chunk 189 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 49 optimal weight: 0.4980 chunk 177 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 182 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 619 ASN ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.132193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.079318 restraints weight = 75493.588| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 5.01 r_work: 0.2940 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.5093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 17422 Z= 0.233 Angle : 0.806 59.200 23660 Z= 0.440 Chirality : 0.040 0.344 2745 Planarity : 0.004 0.065 2906 Dihedral : 3.789 19.990 2434 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.69 % Allowed : 21.50 % Favored : 75.81 % Cbeta Deviations : 0.05 % 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: 2.08 (0.19), residues: 2229 helix: 2.75 (0.15), residues: 1350 sheet: -0.63 (0.43), residues: 159 loop : -0.90 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.002 TRP B 460 HIS 0.006 0.001 HIS C 412 PHE 0.023 0.001 PHE B 515 TYR 0.014 0.001 TYR C 523 ARG 0.025 0.001 ARG B 453 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4061.34 seconds wall clock time: 74 minutes 36.16 seconds (4476.16 seconds total)