Starting phenix.real_space_refine on Tue Nov 19 05:56:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5z_44232/11_2024/9b5z_44232.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5z_44232/11_2024/9b5z_44232.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5z_44232/11_2024/9b5z_44232.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5z_44232/11_2024/9b5z_44232.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5z_44232/11_2024/9b5z_44232.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b5z_44232/11_2024/9b5z_44232.cif" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 128 5.16 5 C 12136 2.51 5 N 3018 2.21 5 O 3398 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 18680 Number of models: 1 Model: "" Number of chains: 8 Chain: "H" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1521 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 194} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 1524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1524 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 194} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3182 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 408, 3167 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 408, 3167 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 3219 Chain: "B" Number of atoms: 3177 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 408, 3166 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 408, 3166 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 3222 Chain: "A" Number of atoms: 3160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3160 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 3180 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 408, 3164 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 408, 3164 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 3215 Chain: "E" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1468 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 186} Chain breaks: 2 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: "G" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1468 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 186} Chain breaks: 2 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: 3 residue: pdb=" N AHIS C 435 " occ=0.86 ... (18 atoms not shown) pdb=" NE2BHIS C 435 " occ=0.14 residue: pdb=" N APHE B 623 " occ=0.46 ... (20 atoms not shown) pdb=" CZ BPHE B 623 " occ=0.54 residue: pdb=" N APHE D 623 " occ=0.62 ... (20 atoms not shown) pdb=" CZ BPHE D 623 " occ=0.38 Time building chain proxies: 15.74, per 1000 atoms: 0.84 Number of scatterers: 18680 At special positions: 0 Unit cell: (113.98, 109.88, 146.78, 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 128 16.00 O 3398 8.00 N 3018 7.00 C 12136 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 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=2.03 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.03 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.60 Conformation dependent library (CDL) restraints added in 3.8 seconds 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4422 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 22 sheets defined 60.8% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'H' and resid 5 through 30 Processing helix chain 'H' and resid 92 through 105 removed outlier: 3.558A pdb=" N TYR H 96 " --> pdb=" O ASP H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 128 removed outlier: 3.954A pdb=" N GLU H 126 " --> pdb=" O ILE H 122 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 163 removed outlier: 4.017A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY H 162 " --> pdb=" O SER H 158 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP H 163 " --> pdb=" O ALA H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 214 Processing helix chain 'F' and resid 6 through 30 Processing helix chain 'F' and resid 92 through 105 removed outlier: 3.612A pdb=" N TYR F 96 " --> pdb=" O ASP F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 128 removed outlier: 3.809A pdb=" N GLU F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 161 removed outlier: 3.699A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 167 removed outlier: 6.710A pdb=" N SER F 165 " --> pdb=" O GLY F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 214 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 Processing helix chain 'C' and resid 461 through 469 removed outlier: 3.521A pdb=" N TYR C 469 " --> pdb=" O GLY C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 515 through 519 removed outlier: 3.781A pdb=" N LEU C 518 " --> pdb=" O PHE C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 546 Processing helix chain 'C' and resid 547 through 551 Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 630 Processing helix chain 'C' and resid 635 through 642 Processing helix chain 'C' and resid 653 through 662 removed outlier: 3.797A pdb=" N GLU C 657 " --> pdb=" O GLY C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 676 removed outlier: 4.192A pdb=" N LYS C 669 " --> pdb=" O ALA C 665 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET C 670 " --> pdb=" O VAL C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 696 Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 742 through 757 Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'C' and resid 788 through 791 Processing helix chain 'C' and resid 792 through 825 removed outlier: 3.550A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 419 removed outlier: 3.938A pdb=" N GLU B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 461 through 469 removed outlier: 3.511A pdb=" N LEU B 467 " --> pdb=" O MET B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.905A 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 547 through 551 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 removed outlier: 3.578A pdb=" N LEU B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.555A pdb=" N GLU B 657 " --> pdb=" O GLY B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 676 removed outlier: 3.617A pdb=" N ASP B 668 " --> pdb=" O ILE B 664 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR B 673 " --> pdb=" O LYS B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 695 removed outlier: 3.548A pdb=" N VAL B 693 " --> pdb=" O GLY B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 714 removed outlier: 3.538A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 792 through 825 Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.832A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG A 420 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.785A 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 630 Processing helix chain 'A' and resid 635 through 642 Processing helix chain 'A' and resid 653 through 661 removed outlier: 3.749A pdb=" N PHE A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 676 removed outlier: 3.679A pdb=" N MET A 670 " --> pdb=" O VAL A 666 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR A 673 " --> pdb=" O LYS A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 742 through 757 Processing helix chain 'A' and resid 757 through 768 Processing helix chain 'A' and resid 788 through 791 Processing helix chain 'A' and resid 792 through 825 Processing helix chain 'D' and resid 416 through 419 removed outlier: 4.325A 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: 3.660A pdb=" N GLU D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.910A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 546 Processing helix chain 'D' and resid 547 through 551 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 626 Processing helix chain 'D' and resid 635 through 642 removed outlier: 3.651A pdb=" N LEU D 639 " --> pdb=" O SER D 635 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 664 through 676 removed outlier: 3.599A pdb=" N TYR D 673 " --> pdb=" O LYS D 669 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET D 674 " --> pdb=" O MET D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 695 removed outlier: 3.880A pdb=" N ALA D 691 " --> pdb=" O ALA D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 788 through 791 Processing helix chain 'D' and resid 792 through 825 removed outlier: 3.505A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 29 Processing helix chain 'E' and resid 92 through 105 Processing helix chain 'E' and resid 105 through 127 removed outlier: 3.944A pdb=" N GLU E 126 " --> pdb=" O ILE E 122 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE E 127 " --> pdb=" O ALA E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 161 removed outlier: 3.734A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 214 removed outlier: 3.526A pdb=" N ILE E 188 " --> pdb=" O ALA E 184 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE E 201 " --> pdb=" O ALA E 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 30 Processing helix chain 'G' and resid 92 through 105 Processing helix chain 'G' and resid 105 through 125 Processing helix chain 'G' and resid 132 through 161 removed outlier: 3.905A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 214 removed outlier: 3.599A pdb=" N ALA G 214 " --> pdb=" O ALA G 210 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 77 through 79 Processing sheet with id=AA2, first strand: chain 'F' and resid 77 through 79 removed outlier: 3.840A pdb=" N CYS F 67 " --> pdb=" O HIS F 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 440 through 444 removed outlier: 6.233A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL C 396 " --> pdb=" O ILE C 474 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ILE C 476 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N THR C 398 " --> pdb=" O ILE C 476 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ALA C 477 " --> pdb=" O ASP C 733 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ASP C 733 " --> pdb=" O ALA C 477 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU C 479 " --> pdb=" O GLY C 731 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLY C 731 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 440 through 444 removed outlier: 6.233A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL C 396 " --> pdb=" O ILE C 474 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ILE C 476 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N THR C 398 " --> pdb=" O ILE C 476 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ALA C 477 " --> pdb=" O ASP C 733 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ASP C 733 " --> pdb=" O ALA C 477 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU C 479 " --> pdb=" O GLY C 731 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLY C 731 " --> pdb=" O LEU C 479 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AA6, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.495A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.368A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 723 " --> pdb=" O ILE C 502 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 439 through 444 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 490 through 491 Processing sheet with id=AB1, first strand: chain 'B' and resid 496 through 498 removed outlier: 4.002A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.457A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.321A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 395 through 399 Processing sheet with id=AB4, first strand: chain 'A' and resid 453 through 454 removed outlier: 3.778A pdb=" N ASP A 454 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE A 459 " --> pdb=" O ASP A 454 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 489 through 491 Processing sheet with id=AB6, first strand: chain 'A' and resid 496 through 498 removed outlier: 3.798A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.490A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 441 through 444 removed outlier: 5.553A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE D 474 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE D 476 " --> pdb=" O THR D 398 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ALA D 477 " --> pdb=" O ASP D 733 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ASP D 733 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LEU D 479 " --> pdb=" O GLY D 731 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLY D 731 " --> pdb=" O LEU D 479 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 441 through 444 removed outlier: 5.553A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE D 474 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE D 476 " --> pdb=" O THR D 398 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ALA D 477 " --> pdb=" O ASP D 733 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ASP D 733 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LEU D 479 " --> pdb=" O GLY D 731 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLY D 731 " --> pdb=" O LEU D 479 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 407 through 408 removed outlier: 3.601A pdb=" N GLU D 422 " --> pdb=" O MET D 407 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.565A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.375A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 77 through 79 Processing sheet with id=AC4, first strand: chain 'G' and resid 77 through 79 1184 hydrogen bonds defined for protein. 3439 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: 6.88 Time building geometry restraints manager: 5.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5772 1.34 - 1.46: 4951 1.46 - 1.58: 8172 1.58 - 1.70: 1 1.70 - 1.82: 208 Bond restraints: 19104 Sorted by residual: bond pdb=" CB PRO H 164 " pdb=" CG PRO H 164 " ideal model delta sigma weight residual 1.492 1.651 -0.159 5.00e-02 4.00e+02 1.02e+01 bond pdb=" N PRO H 164 " pdb=" CD PRO H 164 " ideal model delta sigma weight residual 1.473 1.498 -0.025 1.40e-02 5.10e+03 3.25e+00 bond pdb=" N PRO H 164 " pdb=" CA PRO H 164 " ideal model delta sigma weight residual 1.469 1.447 0.021 1.28e-02 6.10e+03 2.74e+00 bond pdb=" CB GLU A 637 " pdb=" CG GLU A 637 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.21e+00 bond pdb=" CG GLU A 637 " pdb=" CD GLU A 637 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.12e+00 ... (remaining 19099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 25739 3.31 - 6.63: 84 6.63 - 9.94: 9 9.94 - 13.26: 6 13.26 - 16.57: 1 Bond angle restraints: 25839 Sorted by residual: angle pdb=" CA PRO H 164 " pdb=" N PRO H 164 " pdb=" CD PRO H 164 " ideal model delta sigma weight residual 112.00 95.43 16.57 1.40e+00 5.10e-01 1.40e+02 angle pdb=" N PRO H 164 " pdb=" CD PRO H 164 " pdb=" CG PRO H 164 " ideal model delta sigma weight residual 103.20 96.06 7.14 1.50e+00 4.44e-01 2.27e+01 angle pdb=" CB MET C 408 " pdb=" CG MET C 408 " pdb=" SD MET C 408 " ideal model delta sigma weight residual 112.70 125.70 -13.00 3.00e+00 1.11e-01 1.88e+01 angle pdb=" CB MET B 408 " pdb=" CG MET B 408 " pdb=" SD MET B 408 " ideal model delta sigma weight residual 112.70 124.89 -12.19 3.00e+00 1.11e-01 1.65e+01 angle pdb=" CB MET D 708 " pdb=" CG MET D 708 " pdb=" SD MET D 708 " ideal model delta sigma weight residual 112.70 124.60 -11.90 3.00e+00 1.11e-01 1.57e+01 ... (remaining 25834 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 9527 17.67 - 35.33: 1241 35.33 - 53.00: 341 53.00 - 70.67: 60 70.67 - 88.34: 30 Dihedral angle restraints: 11199 sinusoidal: 4271 harmonic: 6928 Sorted by residual: dihedral pdb=" CB CYS A 718 " pdb=" SG CYS A 718 " pdb=" SG CYS A 773 " pdb=" CB CYS A 773 " ideal model delta sinusoidal sigma weight residual 93.00 163.98 -70.98 1 1.00e+01 1.00e-02 6.47e+01 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 93.00 143.90 -50.90 1 1.00e+01 1.00e-02 3.55e+01 dihedral pdb=" CB CYS D 718 " pdb=" SG CYS D 718 " pdb=" SG CYS D 773 " pdb=" CB CYS D 773 " ideal model delta sinusoidal sigma weight residual 93.00 139.44 -46.44 1 1.00e+01 1.00e-02 2.98e+01 ... (remaining 11196 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2355 0.048 - 0.096: 456 0.096 - 0.144: 89 0.144 - 0.192: 3 0.192 - 0.240: 2 Chirality restraints: 2905 Sorted by residual: chirality pdb=" CA PRO H 164 " pdb=" N PRO H 164 " pdb=" C PRO H 164 " pdb=" CB PRO H 164 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CG LEU A 811 " pdb=" CB LEU A 811 " pdb=" CD1 LEU A 811 " pdb=" CD2 LEU A 811 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA ILE C 476 " pdb=" N ILE C 476 " pdb=" C ILE C 476 " pdb=" CB ILE C 476 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.95e-01 ... (remaining 2902 not shown) Planarity restraints: 3198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP H 163 " 0.083 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO H 164 " -0.194 5.00e-02 4.00e+02 pdb=" CA PRO H 164 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO H 164 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 644 " -0.012 2.00e-02 2.50e+03 2.45e-02 5.99e+00 pdb=" CD GLU C 644 " 0.042 2.00e-02 2.50e+03 pdb=" OE1 GLU C 644 " -0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU C 644 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 204 " -0.130 9.50e-02 1.11e+02 5.83e-02 2.45e+00 pdb=" NE ARG G 204 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG G 204 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG G 204 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG G 204 " -0.001 2.00e-02 2.50e+03 ... (remaining 3195 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3396 2.76 - 3.30: 17983 3.30 - 3.83: 32653 3.83 - 4.37: 36848 4.37 - 4.90: 63727 Nonbonded interactions: 154607 Sorted by model distance: nonbonded pdb=" O SER H 105 " pdb=" OG SER H 105 " model vdw 2.227 3.040 nonbonded pdb=" N GLU C 637 " pdb=" OE1 GLU C 637 " model vdw 2.258 3.120 nonbonded pdb=" N GLU A 644 " pdb=" OE1 GLU A 644 " model vdw 2.259 3.120 nonbonded pdb=" NH2 ARG A 420 " pdb=" OH TYR A 421 " model vdw 2.305 3.120 nonbonded pdb=" OD2 ASP D 454 " pdb=" OG1 THR D 457 " model vdw 2.306 3.040 ... (remaining 154602 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 434 or resid 436 through 438 o \ r (resid 439 and (name N or name CA or name C or name O or name CB or name CG )) \ or resid 440 through 575 or (resid 576 and (name N or name CA or name C or name \ O or name CB )) or resid 577 through 622 or resid 624 through 626 or (resid 627 \ and (name N or name CA or name C or name O or name CB )) or resid 628 through 7 \ 63 or resid 765 through 812 or (resid 813 and (name N or name CA or name C or na \ me O or name CB )) or resid 814 through 818 or (resid 819 through 820 and (name \ N or name CA or name C or name O or name CB )) or resid 821 through 825)) selection = (chain 'B' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 434 or resid 436 through 438 o \ r (resid 439 and (name N or name CA or name C or name O or name CB or name CG )) \ or resid 440 through 508 or (resid 509 and (name N or name CA or name C or name \ O or name CB )) or resid 510 or (resid 511 and (name N or name CA or name C or \ name O or name CB )) or resid 512 through 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 622 or \ resid 624 through 626 or (resid 627 and (name N or name CA or name C or name O \ or name CB )) or resid 628 through 763 or resid 765 through 773 or (resid 784 an \ d (name N or name CA or name C or name O or name CB )) or resid 785 through 825) \ ) selection = (chain 'C' and (resid 393 through 434 or resid 436 through 593 or (resid 594 and \ (name N or name CA or name C or name O or name CB )) or resid 595 through 622 o \ r resid 624 through 626 or (resid 627 and (name N or name CA or name C or name O \ or name CB )) or resid 628 through 666 or (resid 667 and (name N or name CA or \ name C or name O or name CB )) or resid 668 through 763 or resid 765 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 820 and (name N or name CA or name C or n \ ame O or name CB )) or resid 821 through 825)) selection = (chain 'D' and (resid 393 through 434 or resid 436 through 508 or (resid 509 and \ (name N or name CA or name C or name O or name CB )) or resid 510 or (resid 511 \ and (name N or name CA or name C or name O or name CB )) or resid 512 through 5 \ 75 or (resid 576 and (name N or name CA or name C or name O or name CB )) or res \ id 577 through 593 or (resid 594 and (name N or name CA or name C or name O or n \ ame CB )) or resid 595 through 622 or resid 624 through 666 or (resid 667 and (n \ ame N or name CA or name C or name O or name CB )) or resid 668 through 763 or r \ esid 765 through 773 or (resid 784 and (name N or name CA or name C or name O or \ name CB )) or resid 785 through 825)) } ncs_group { reference = (chain 'E' and resid 5 through 214) selection = (chain 'F' and (resid 5 through 41 or resid 55 through 162 or resid 173 through \ 214)) selection = (chain 'G' and resid 5 through 214) selection = (chain 'H' and (resid 5 through 41 or resid 55 through 162 or resid 173 through \ 214)) } 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=0.12 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: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.850 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 49.040 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.100 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:12.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.159 19104 Z= 0.206 Angle : 0.560 16.575 25839 Z= 0.292 Chirality : 0.038 0.240 2905 Planarity : 0.004 0.113 3198 Dihedral : 17.446 88.337 6741 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.62 % Favored : 97.33 % Rotamer: Outliers : 2.18 % Allowed : 32.15 % Favored : 65.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.35 % 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: 1.82 (0.17), residues: 2373 helix: 2.53 (0.14), residues: 1375 sheet: -0.83 (0.35), residues: 200 loop : -0.62 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 671 HIS 0.010 0.001 HIS H 60 PHE 0.019 0.001 PHE E 127 TYR 0.022 0.001 TYR A 673 ARG 0.012 0.000 ARG D 684 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 273 time to evaluate : 2.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 166 LYS cc_start: 0.7153 (OUTLIER) cc_final: 0.6743 (mptt) REVERT: C 642 GLN cc_start: 0.7759 (pp30) cc_final: 0.7423 (pp30) REVERT: C 715 ARG cc_start: 0.7516 (mmp80) cc_final: 0.7281 (mpt180) REVERT: A 420 ARG cc_start: 0.7599 (mtm-85) cc_final: 0.6878 (mpp-170) REVERT: A 756 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8055 (mp10) REVERT: E 10 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8183 (mmm) REVERT: G 99 ARG cc_start: 0.6918 (mtt180) cc_final: 0.6592 (ptp-110) outliers start: 43 outliers final: 34 residues processed: 309 average time/residue: 1.3749 time to fit residues: 477.7533 Evaluate side-chains 305 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 268 time to evaluate : 1.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 166 LYS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 738 LYS Chi-restraints excluded: chain C residue 755 GLU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 755 GLU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 756 GLN Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 818 SER Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 155 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 0.6980 chunk 177 optimal weight: 0.0870 chunk 98 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 119 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 136 optimal weight: 0.8980 chunk 212 optimal weight: 3.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 205 HIS F 149 ASN F 160 ASN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 HIS G 160 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19104 Z= 0.167 Angle : 0.512 10.133 25839 Z= 0.270 Chirality : 0.039 0.188 2905 Planarity : 0.003 0.035 3198 Dihedral : 5.171 58.369 2652 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.33 % Favored : 97.63 % Rotamer: Outliers : 3.96 % Allowed : 28.80 % Favored : 67.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.35 % 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: 2.18 (0.17), residues: 2373 helix: 2.84 (0.14), residues: 1397 sheet: -0.84 (0.38), residues: 156 loop : -0.62 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 766 HIS 0.012 0.001 HIS H 60 PHE 0.013 0.001 PHE B 438 TYR 0.018 0.001 TYR A 673 ARG 0.008 0.000 ARG D 684 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 319 time to evaluate : 2.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7559 (tp) REVERT: H 78 LYS cc_start: 0.8101 (tmmt) cc_final: 0.7254 (ttmt) REVERT: F 31 ASP cc_start: 0.7779 (OUTLIER) cc_final: 0.7435 (m-30) REVERT: F 65 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.6820 (ppt-90) REVERT: F 86 ASP cc_start: 0.5260 (OUTLIER) cc_final: 0.4619 (m-30) REVERT: F 167 SER cc_start: 0.6748 (OUTLIER) cc_final: 0.6474 (m) REVERT: C 463 MET cc_start: 0.8218 (mmm) cc_final: 0.7985 (mpp) REVERT: C 642 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.7345 (pp30) REVERT: C 671 TRP cc_start: 0.7819 (t-100) cc_final: 0.7499 (t-100) REVERT: B 506 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8369 (ttmm) REVERT: A 439 LYS cc_start: 0.7858 (pmtt) cc_final: 0.7534 (pptt) REVERT: D 407 MET cc_start: 0.8112 (ptt) cc_final: 0.7880 (mtm) REVERT: D 458 LYS cc_start: 0.7853 (tppt) cc_final: 0.7337 (tppp) REVERT: D 818 SER cc_start: 0.8018 (t) cc_final: 0.7782 (p) REVERT: E 68 CYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7479 (m) outliers start: 78 outliers final: 30 residues processed: 375 average time/residue: 1.2906 time to fit residues: 547.4082 Evaluate side-chains 316 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 278 time to evaluate : 2.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 642 GLN Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 818 SER Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 756 GLN Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 175 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 0.0980 chunk 65 optimal weight: 0.9990 chunk 176 optimal weight: 0.7980 chunk 144 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 212 optimal weight: 0.4980 chunk 229 optimal weight: 3.9990 chunk 189 optimal weight: 9.9990 chunk 211 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 170 optimal weight: 0.8980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN A 726 ASN E 207 GLN G 132 HIS G 160 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 19104 Z= 0.159 Angle : 0.503 10.940 25839 Z= 0.261 Chirality : 0.039 0.193 2905 Planarity : 0.003 0.036 3198 Dihedral : 3.818 42.396 2610 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.33 % Favored : 97.63 % Rotamer: Outliers : 3.91 % Allowed : 28.75 % Favored : 67.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.35 % 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: 2.27 (0.17), residues: 2373 helix: 2.92 (0.14), residues: 1401 sheet: -0.73 (0.40), residues: 144 loop : -0.65 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 178 HIS 0.010 0.001 HIS H 60 PHE 0.010 0.001 PHE A 584 TYR 0.011 0.001 TYR C 673 ARG 0.005 0.000 ARG D 684 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 308 time to evaluate : 2.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 60 HIS cc_start: 0.7211 (p-80) cc_final: 0.6991 (p90) REVERT: F 31 ASP cc_start: 0.7671 (OUTLIER) cc_final: 0.7356 (m-30) REVERT: F 65 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.6760 (ppt-90) REVERT: F 149 ASN cc_start: 0.8398 (OUTLIER) cc_final: 0.8176 (t0) REVERT: F 167 SER cc_start: 0.6740 (OUTLIER) cc_final: 0.6488 (m) REVERT: C 463 MET cc_start: 0.8228 (mmm) cc_final: 0.7733 (mpp) REVERT: C 642 GLN cc_start: 0.7713 (pp30) cc_final: 0.7491 (pp30) REVERT: A 413 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6690 (mm-30) REVERT: A 674 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.8156 (mtm) REVERT: A 756 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7972 (mp10) REVERT: D 407 MET cc_start: 0.8127 (ptt) cc_final: 0.7867 (mtm) REVERT: D 458 LYS cc_start: 0.7850 (tppt) cc_final: 0.7334 (tppp) REVERT: E 97 PHE cc_start: 0.7843 (t80) cc_final: 0.7499 (t80) outliers start: 77 outliers final: 33 residues processed: 360 average time/residue: 1.2900 time to fit residues: 527.3143 Evaluate side-chains 318 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 278 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 199 HIS Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 629 MET Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 755 GLU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 756 GLN Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 175 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 0.9990 chunk 160 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 101 optimal weight: 0.5980 chunk 142 optimal weight: 9.9990 chunk 213 optimal weight: 2.9990 chunk 226 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 202 optimal weight: 7.9990 chunk 60 optimal weight: 0.4980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 79 GLN ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 HIS G 160 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1720 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: