Starting phenix.real_space_refine on Tue Apr 9 16:37:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3u_17395/04_2024/8p3u_17395_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3u_17395/04_2024/8p3u_17395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3u_17395/04_2024/8p3u_17395.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3u_17395/04_2024/8p3u_17395.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3u_17395/04_2024/8p3u_17395_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3u_17395/04_2024/8p3u_17395_neut.pdb" } resolution = 3.77 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= 0.039 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 96 5.16 5 C 11078 2.51 5 N 2735 2.21 5 O 2979 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 427": "OE1" <-> "OE2" Residue "A ARG 449": "NH1" <-> "NH2" Residue "A GLU 482": "OE1" <-> "OE2" Residue "A GLU 520": "OE1" <-> "OE2" Residue "A ARG 711": "NH1" <-> "NH2" Residue "A GLU 751": "OE1" <-> "OE2" Residue "B GLU 423": "OE1" <-> "OE2" Residue "B ARG 449": "NH1" <-> "NH2" Residue "B GLU 482": "OE1" <-> "OE2" Residue "B GLU 483": "OE1" <-> "OE2" Residue "B GLU 520": "OE1" <-> "OE2" Residue "B GLU 623": "OE1" <-> "OE2" Residue "B GLU 633": "OE1" <-> "OE2" Residue "B GLU 684": "OE1" <-> "OE2" Residue "C GLU 418": "OE1" <-> "OE2" Residue "C GLU 427": "OE1" <-> "OE2" Residue "C ARG 449": "NH1" <-> "NH2" Residue "C GLU 482": "OE1" <-> "OE2" Residue "C GLU 701": "OE1" <-> "OE2" Residue "D PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 427": "OE1" <-> "OE2" Residue "D ARG 449": "NH1" <-> "NH2" Residue "D GLU 482": "OE1" <-> "OE2" Residue "D GLU 483": "OE1" <-> "OE2" Residue "D GLU 520": "OE1" <-> "OE2" Residue "D ARG 690": "NH1" <-> "NH2" Residue "D GLU 701": "OE1" <-> "OE2" Residue "F GLU 202": "OE1" <-> "OE2" Residue "G GLU 70": "OE1" <-> "OE2" Residue "G GLU 95": "OE1" <-> "OE2" Residue "G GLU 190": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 16888 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2850 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 372} Chain breaks: 4 Unresolved non-hydrogen bonds: 203 Unresolved non-hydrogen angles: 244 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 6, 'GLU:plan': 13, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 133 Chain: "B" Number of atoms: 2917 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 385, 2886 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 371} Chain breaks: 4 Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 6, 'GLU:plan': 8, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 94 Conformer: "B" Number of residues, atoms: 385, 2886 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 371} Chain breaks: 4 Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 6, 'GLU:plan': 8, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 94 bond proxies already assigned to first conformer: 2915 Chain: "C" Number of atoms: 2848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2848 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 372} Chain breaks: 4 Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 174 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'GLU:plan': 13, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 120 Chain: "D" Number of atoms: 2860 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 381, 2829 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 369} Chain breaks: 4 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 7, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 112 Conformer: "B" Number of residues, atoms: 381, 2829 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 369} Chain breaks: 4 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 7, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 112 bond proxies already assigned to first conformer: 2855 Chain: "E" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1357 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1348 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 4 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1351 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "H" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1357 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N APHE B 570 " occ=0.59 ... (20 atoms not shown) pdb=" CZ BPHE B 570 " occ=0.41 residue: pdb=" N AGLN B 582 " occ=0.24 ... (16 atoms not shown) pdb=" NE2BGLN B 582 " occ=0.76 residue: pdb=" N APHE B 619 " occ=0.37 ... (20 atoms not shown) pdb=" CZ BPHE B 619 " occ=0.63 residue: pdb=" N APHE D 570 " occ=0.71 ... (20 atoms not shown) pdb=" CZ BPHE D 570 " occ=0.29 residue: pdb=" N AGLN D 582 " occ=0.10 ... (16 atoms not shown) pdb=" NE2BGLN D 582 " occ=0.90 residue: pdb=" N APHE D 619 " occ=0.68 ... (20 atoms not shown) pdb=" CZ BPHE D 619 " occ=0.32 Time building chain proxies: 11.62, per 1000 atoms: 0.69 Number of scatterers: 16888 At special positions: 0 Unit cell: (116.6, 117.925, 136.475, 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 96 16.00 O 2979 8.00 N 2735 7.00 C 11078 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 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 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 G 40 " - pdb=" SG CYS G 68 " distance=2.03 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.04 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.82 Conformation dependent library (CDL) restraints added in 4.0 seconds 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4102 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 26 sheets defined 61.5% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 407 through 411 removed outlier: 3.593A pdb=" N GLN A 410 " --> pdb=" O ASN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 415 removed outlier: 4.163A pdb=" N ASP A 415 " --> pdb=" O GLU A 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 412 through 415' Processing helix chain 'A' and resid 419 through 433 Processing helix chain 'A' and resid 458 through 465 Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 518 through 542 removed outlier: 3.549A pdb=" N TRP A 522 " --> pdb=" O ALA A 518 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET A 523 " --> pdb=" O TYR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 581 removed outlier: 3.878A pdb=" N MET A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 622 Processing helix chain 'A' and resid 649 through 657 Processing helix chain 'A' and resid 660 through 673 Processing helix chain 'A' and resid 681 through 692 Processing helix chain 'A' and resid 702 through 710 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 753 through 764 Processing helix chain 'A' and resid 788 through 814 removed outlier: 3.540A pdb=" N MET A 803 " --> pdb=" O LEU A 799 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 804 " --> pdb=" O GLY A 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 411 removed outlier: 3.587A pdb=" N GLN B 410 " --> pdb=" O ASN B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 415 No H-bonds generated for 'chain 'B' and resid 413 through 415' Processing helix chain 'B' and resid 419 through 433 Processing helix chain 'B' and resid 457 through 465 Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 518 through 542 removed outlier: 3.793A pdb=" N CYS B 524 " --> pdb=" O GLU B 520 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE B 542 " --> pdb=" O LEU B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 581 Processing helix chain 'B' and resid 591 through 623 Processing helix chain 'B' and resid 631 through 638 Processing helix chain 'B' and resid 649 through 657 Processing helix chain 'B' and resid 660 through 673 removed outlier: 3.556A pdb=" N SER B 672 " --> pdb=" O THR B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 692 Processing helix chain 'B' and resid 702 through 711 Processing helix chain 'B' and resid 738 through 752 Processing helix chain 'B' and resid 753 through 763 Processing helix chain 'B' and resid 784 through 787 removed outlier: 3.586A pdb=" N ASN B 787 " --> pdb=" O SER B 784 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 784 through 787' Processing helix chain 'B' and resid 788 through 815 removed outlier: 3.978A pdb=" N PHE B 792 " --> pdb=" O VAL B 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 411 removed outlier: 3.529A pdb=" N GLN C 410 " --> pdb=" O ASN C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 415 removed outlier: 4.121A pdb=" N ASP C 415 " --> pdb=" O GLU C 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 412 through 415' Processing helix chain 'C' and resid 419 through 433 Processing helix chain 'C' and resid 458 through 465 Processing helix chain 'C' and resid 478 through 483 Processing helix chain 'C' and resid 511 through 515 removed outlier: 3.511A pdb=" N LEU C 514 " --> pdb=" O PHE C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 540 Processing helix chain 'C' and resid 568 through 581 Processing helix chain 'C' and resid 591 through 622 Processing helix chain 'C' and resid 632 through 638 removed outlier: 3.533A pdb=" N GLN C 638 " --> pdb=" O ASP C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 657 Processing helix chain 'C' and resid 660 through 672 Processing helix chain 'C' and resid 681 through 692 Processing helix chain 'C' and resid 702 through 711 Processing helix chain 'C' and resid 738 through 752 Processing helix chain 'C' and resid 753 through 764 Processing helix chain 'C' and resid 788 through 814 removed outlier: 3.528A pdb=" N PHE C 792 " --> pdb=" O VAL C 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 411 removed outlier: 3.579A pdb=" N GLN D 410 " --> pdb=" O ASN D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 415 removed outlier: 4.211A pdb=" N ASP D 415 " --> pdb=" O GLU D 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 412 through 415' Processing helix chain 'D' and resid 419 through 433 Processing helix chain 'D' and resid 457 through 466 Processing helix chain 'D' and resid 478 through 483 Processing helix chain 'D' and resid 511 through 515 removed outlier: 3.515A pdb=" N LEU D 514 " --> pdb=" O PHE D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 542 removed outlier: 3.744A pdb=" N PHE D 542 " --> pdb=" O LEU D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 581 Processing helix chain 'D' and resid 591 through 622 Processing helix chain 'D' and resid 631 through 638 Processing helix chain 'D' and resid 649 through 657 Processing helix chain 'D' and resid 660 through 673 Processing helix chain 'D' and resid 681 through 692 Processing helix chain 'D' and resid 702 through 711 Processing helix chain 'D' and resid 738 through 752 Processing helix chain 'D' and resid 753 through 764 Processing helix chain 'D' and resid 785 through 787 No H-bonds generated for 'chain 'D' and resid 785 through 787' Processing helix chain 'D' and resid 788 through 815 removed outlier: 3.786A pdb=" N PHE D 792 " --> pdb=" O VAL D 788 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 30 Processing helix chain 'E' and resid 93 through 105 Processing helix chain 'E' and resid 105 through 128 removed outlier: 4.315A pdb=" N GLU E 126 " --> pdb=" O VAL E 122 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE E 127 " --> pdb=" O ALA E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 162 removed outlier: 4.242A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 209 removed outlier: 3.688A pdb=" N TYR E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 30 removed outlier: 3.590A pdb=" N VAL F 15 " --> pdb=" O LEU F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 94 No H-bonds generated for 'chain 'F' and resid 93 through 94' Processing helix chain 'F' and resid 96 through 96 No H-bonds generated for 'chain 'F' and resid 96 through 96' Processing helix chain 'F' and resid 97 through 105 Processing helix chain 'F' and resid 105 through 124 removed outlier: 3.648A pdb=" N ILE F 109 " --> pdb=" O SER F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 162 removed outlier: 3.789A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 209 removed outlier: 3.710A pdb=" N TYR F 180 " --> pdb=" O GLY F 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 30 Processing helix chain 'G' and resid 93 through 105 removed outlier: 3.548A pdb=" N ARG G 99 " --> pdb=" O GLU G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 128 removed outlier: 3.508A pdb=" N CYS G 121 " --> pdb=" O PHE G 117 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLU G 126 " --> pdb=" O VAL G 122 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N PHE G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 162 removed outlier: 4.296A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 209 removed outlier: 3.590A pdb=" N TYR G 180 " --> pdb=" O GLY G 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 30 Processing helix chain 'H' and resid 93 through 105 Processing helix chain 'H' and resid 105 through 126 removed outlier: 4.045A pdb=" N GLU H 126 " --> pdb=" O VAL H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 162 removed outlier: 4.042A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 209 removed outlier: 3.605A pdb=" N TYR H 180 " --> pdb=" O GLY H 176 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 436 through 440 removed outlier: 6.622A pdb=" N TYR A 391 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLU A 439 " --> pdb=" O TYR A 391 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N VAL A 393 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA3, first strand: chain 'A' and resid 447 through 449 removed outlier: 3.671A pdb=" N ALA A 448 " --> pdb=" O ASN A 457 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 485 through 487 Processing sheet with id=AA5, first strand: chain 'A' and resid 492 through 494 removed outlier: 4.057A pdb=" N MET A 492 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 643 through 644 removed outlier: 6.557A pdb=" N GLY A 644 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N GLU A 701 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 436 through 440 removed outlier: 6.758A pdb=" N TYR B 391 " --> pdb=" O ARG B 437 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLU B 439 " --> pdb=" O TYR B 391 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N VAL B 393 " --> pdb=" O GLU B 439 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 470 " --> pdb=" O ILE B 392 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 403 through 404 Processing sheet with id=AA9, first strand: chain 'B' and resid 485 through 487 Processing sheet with id=AB1, first strand: chain 'B' and resid 492 through 494 removed outlier: 3.877A pdb=" N MET B 492 " --> pdb=" O TYR B 728 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 642 through 644 removed outlier: 6.481A pdb=" N ALA B 642 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU B 699 " --> pdb=" O ALA B 642 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLY B 644 " --> pdb=" O LEU B 699 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N GLU B 701 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ILE B 498 " --> pdb=" O VAL B 719 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 436 through 440 removed outlier: 6.525A pdb=" N TYR C 391 " --> pdb=" O ARG C 437 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLU C 439 " --> pdb=" O TYR C 391 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N VAL C 393 " --> pdb=" O GLU C 439 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 403 through 404 Processing sheet with id=AB5, first strand: chain 'C' and resid 447 through 450 removed outlier: 3.753A pdb=" N ALA C 448 " --> pdb=" O ASN C 457 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA C 455 " --> pdb=" O ASP C 450 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 485 through 487 Processing sheet with id=AB7, first strand: chain 'C' and resid 492 through 494 removed outlier: 3.847A pdb=" N MET C 492 " --> pdb=" O TYR C 728 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 642 through 644 removed outlier: 6.541A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR C 698 " --> pdb=" O MET C 499 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 436 through 440 removed outlier: 6.397A pdb=" N TYR D 391 " --> pdb=" O ARG D 437 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N GLU D 439 " --> pdb=" O TYR D 391 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL D 393 " --> pdb=" O GLU D 439 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL D 470 " --> pdb=" O ILE D 392 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 403 through 404 Processing sheet with id=AC2, first strand: chain 'D' and resid 485 through 487 Processing sheet with id=AC3, first strand: chain 'D' and resid 492 through 494 removed outlier: 3.836A pdb=" N MET D 492 " --> pdb=" O TYR D 728 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 642 through 644 removed outlier: 6.620A pdb=" N ALA D 642 " --> pdb=" O ALA D 697 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LEU D 699 " --> pdb=" O ALA D 642 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLY D 644 " --> pdb=" O LEU D 699 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N GLU D 701 " --> pdb=" O GLY D 644 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE D 498 " --> pdb=" O VAL D 719 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 77 through 79 removed outlier: 4.031A pdb=" N LYS E 78 " --> pdb=" O THR E 66 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR E 66 " --> pdb=" O LYS E 78 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 34 through 38 Processing sheet with id=AC7, first strand: chain 'G' and resid 77 through 79 removed outlier: 4.126A pdb=" N LYS G 78 " --> pdb=" O THR G 66 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR G 66 " --> pdb=" O LYS G 78 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 77 through 79 1107 hydrogen bonds defined for protein. 3230 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: 5.99 Time building geometry restraints manager: 7.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2617 1.32 - 1.44: 4983 1.44 - 1.57: 9525 1.57 - 1.70: 0 1.70 - 1.83: 156 Bond restraints: 17281 Sorted by residual: bond pdb=" C SER A 631 " pdb=" O SER A 631 " ideal model delta sigma weight residual 1.235 1.307 -0.072 1.26e-02 6.30e+03 3.26e+01 bond pdb=" C TYR D 391 " pdb=" O TYR D 391 " ideal model delta sigma weight residual 1.234 1.291 -0.057 1.34e-02 5.57e+03 1.82e+01 bond pdb=" N VAL C 484 " pdb=" CA VAL C 484 " ideal model delta sigma weight residual 1.456 1.497 -0.040 9.50e-03 1.11e+04 1.80e+01 bond pdb=" C ILE D 641 " pdb=" O ILE D 641 " ideal model delta sigma weight residual 1.234 1.282 -0.048 1.17e-02 7.31e+03 1.68e+01 bond pdb=" N VAL D 484 " pdb=" CA VAL D 484 " ideal model delta sigma weight residual 1.460 1.494 -0.034 8.60e-03 1.35e+04 1.59e+01 ... (remaining 17276 not shown) Histogram of bond angle deviations from ideal: 87.04 - 96.53: 4 96.53 - 106.02: 339 106.02 - 115.50: 10285 115.50 - 124.99: 12365 124.99 - 134.48: 470 Bond angle restraints: 23463 Sorted by residual: angle pdb=" N LEU A 635 " pdb=" CA LEU A 635 " pdb=" C LEU A 635 " ideal model delta sigma weight residual 112.54 97.99 14.55 1.22e+00 6.72e-01 1.42e+02 angle pdb=" C LYS A 637 " pdb=" CA LYS A 637 " pdb=" CB LYS A 637 " ideal model delta sigma weight residual 110.42 87.04 23.38 1.99e+00 2.53e-01 1.38e+02 angle pdb=" C THR A 639 " pdb=" CA THR A 639 " pdb=" CB THR A 639 " ideal model delta sigma weight residual 110.36 95.23 15.13 1.78e+00 3.16e-01 7.23e+01 angle pdb=" C GLU C 630 " pdb=" CA GLU C 630 " pdb=" CB GLU C 630 " ideal model delta sigma weight residual 110.42 93.95 16.47 1.99e+00 2.53e-01 6.85e+01 angle pdb=" N ILE A 641 " pdb=" CA ILE A 641 " pdb=" C ILE A 641 " ideal model delta sigma weight residual 109.34 93.67 15.67 2.08e+00 2.31e-01 5.67e+01 ... (remaining 23458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.31: 8587 16.31 - 32.61: 992 32.61 - 48.92: 254 48.92 - 65.23: 64 65.23 - 81.53: 11 Dihedral angle restraints: 9908 sinusoidal: 3483 harmonic: 6425 Sorted by residual: dihedral pdb=" C LYS A 637 " pdb=" N LYS A 637 " pdb=" CA LYS A 637 " pdb=" CB LYS A 637 " ideal model delta harmonic sigma weight residual -122.60 -94.85 -27.75 0 2.50e+00 1.60e-01 1.23e+02 dihedral pdb=" CB CYS E 67 " pdb=" SG CYS E 67 " pdb=" SG CYS E 77 " pdb=" CB CYS E 77 " ideal model delta sinusoidal sigma weight residual 93.00 37.88 55.12 1 1.00e+01 1.00e-02 4.11e+01 dihedral pdb=" C GLU C 630 " pdb=" N GLU C 630 " pdb=" CA GLU C 630 " pdb=" CB GLU C 630 " ideal model delta harmonic sigma weight residual -122.60 -106.57 -16.03 0 2.50e+00 1.60e-01 4.11e+01 ... (remaining 9905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1796 0.101 - 0.201: 842 0.201 - 0.302: 58 0.302 - 0.403: 13 0.403 - 0.503: 3 Chirality restraints: 2712 Sorted by residual: chirality pdb=" CA ILE B 500 " pdb=" N ILE B 500 " pdb=" C ILE B 500 " pdb=" CB ILE B 500 " both_signs ideal model delta sigma weight residual False 2.43 2.94 -0.50 2.00e-01 2.50e+01 6.33e+00 chirality pdb=" CA GLU A 630 " pdb=" N GLU A 630 " pdb=" C GLU A 630 " pdb=" CB GLU A 630 " both_signs ideal model delta sigma weight residual False 2.51 2.98 -0.47 2.00e-01 2.50e+01 5.51e+00 chirality pdb=" CA LYS A 637 " pdb=" N LYS A 637 " pdb=" C LYS A 637 " pdb=" CB LYS A 637 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.32e+00 ... (remaining 2709 not shown) Planarity restraints: 2882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 630 " -0.037 2.00e-02 2.50e+03 7.69e-02 5.91e+01 pdb=" C GLU A 630 " 0.133 2.00e-02 2.50e+03 pdb=" O GLU A 630 " -0.050 2.00e-02 2.50e+03 pdb=" N SER A 631 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 632 " -0.025 2.00e-02 2.50e+03 5.24e-02 2.75e+01 pdb=" C ALA A 632 " 0.091 2.00e-02 2.50e+03 pdb=" O ALA A 632 " -0.035 2.00e-02 2.50e+03 pdb=" N GLU A 633 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 633 " -0.024 2.00e-02 2.50e+03 5.08e-02 2.59e+01 pdb=" C GLU A 633 " 0.088 2.00e-02 2.50e+03 pdb=" O GLU A 633 " -0.033 2.00e-02 2.50e+03 pdb=" N ASP A 634 " -0.030 2.00e-02 2.50e+03 ... (remaining 2879 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 715 2.71 - 3.26: 17907 3.26 - 3.81: 27007 3.81 - 4.35: 35054 4.35 - 4.90: 57095 Nonbonded interactions: 137778 Sorted by model distance: nonbonded pdb=" O ILE A 629 " pdb=" N SER A 631 " model vdw 2.166 2.520 nonbonded pdb=" O PHE D 580 " pdb=" OG1 THR D 605 " model vdw 2.170 2.440 nonbonded pdb=" O LYS B 501 " pdb=" O LYS B 502 " model vdw 2.220 3.040 nonbonded pdb=" OG SER A 631 " pdb=" N ALA A 632 " model vdw 2.228 2.520 nonbonded pdb=" O ALA A 636 " pdb=" N GLN A 638 " model vdw 2.232 2.520 ... (remaining 137773 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 390 through 391 and (name N or name CA or name C or name \ O or name CB )) or resid 392 through 414 or (resid 415 through 416 and (name N o \ r name CA or name C or name O or name CB )) or resid 417 through 429 or (resid 4 \ 30 and (name N or name CA or name C or name O or name CB )) or resid 431 through \ 444 or (resid 445 and (name N or name CA or name C or name O or name CB )) or r \ esid 446 through 502 or resid 509 through 546 or resid 567 through 569 or resid \ 571 through 581 or resid 583 through 618 or resid 620 through 622 or resid 629 t \ hrough 664 or (resid 665 and (name N or name CA or name C or name O or name CB ) \ ) or resid 666 through 767 or resid 782 through 815)) selection = (chain 'B' and ((resid 390 through 391 and (name N or name CA or name C or name \ O or name CB )) or resid 392 through 398 or (resid 399 and (name N or name CA or \ name C or name O or name CB )) or resid 400 through 403 or (resid 404 and (name \ N or name CA or name C or name O or name CB )) or resid 405 through 415 or (res \ id 416 and (name N or name CA or name C or name O or name CB )) or resid 417 thr \ ough 429 or (resid 430 and (name N or name CA or name C or name O or name CB )) \ or resid 431 through 444 or (resid 445 and (name N or name CA or name C or name \ O or name CB )) or resid 446 through 461 or (resid 462 and (name N or name CA or \ name C or name O or name CB )) or resid 463 through 500 or (resid 501 through 5 \ 02 and (name N or name CA or name C or name O or name CB )) or resid 509 through \ 545 or (resid 566 and (name N or name CA or name C or name O or name CB )) or r \ esid 567 through 569 or resid 571 through 581 or resid 583 through 618 or resid \ 620 through 622 or resid 629 through 632 or (resid 633 through 634 and (name N o \ r name CA or name C or name O or name CB )) or resid 635 through 658 or (resid 6 \ 59 and (name N or name CA or name C or name O or name CB )) or resid 660 through \ 664 or (resid 665 and (name N or name CA or name C or name O or name CB )) or r \ esid 666 through 683 or (resid 684 and (name N or name CA or name C or name O or \ name CB )) or resid 685 through 687 or (resid 688 and (name N or name CA or nam \ e C or name O or name CB )) or resid 689 through 690 or (resid 691 through 693 a \ nd (name N or name CA or name C or name O or name CB )) or resid 694 through 705 \ or (resid 706 and (name N or name CA or name C or name O or name CB )) or resid \ 707 through 767 or resid 782 through 813 or (resid 814 through 815 and (name N \ or name CA or name C or name O or name CB )))) selection = (chain 'C' and ((resid 390 through 391 and (name N or name CA or name C or name \ O or name CB )) or resid 392 through 398 or (resid 399 and (name N or name CA or \ name C or name O or name CB )) or resid 400 through 415 or (resid 416 and (name \ N or name CA or name C or name O or name CB )) or resid 417 through 466 or (res \ id 467 through 469 and (name N or name CA or name C or name O or name CB )) or r \ esid 470 through 502 or resid 509 through 546 or resid 567 through 569 or resid \ 571 through 581 or resid 583 through 618 or resid 620 through 622 or resid 629 t \ hrough 633 or (resid 634 and (name N or name CA or name C or name O or name CB ) \ ) or resid 635 through 687 or (resid 688 and (name N or name CA or name C or nam \ e O or name CB )) or resid 689 through 691 or (resid 692 through 693 and (name N \ or name CA or name C or name O or name CB )) or resid 694 through 708 or (resid \ 709 and (name N or name CA or name C or name O or name CB )) or resid 710 throu \ gh 815)) selection = (chain 'D' and (resid 390 through 444 or (resid 445 and (name N or name CA or na \ me C or name O or name CB )) or resid 446 through 466 or (resid 467 through 469 \ and (name N or name CA or name C or name O or name CB )) or resid 470 through 54 \ 5 or (resid 566 and (name N or name CA or name C or name O or name CB )) or resi \ d 567 through 569 or resid 571 through 581 or resid 583 through 618 or resid 620 \ through 658 or (resid 659 and (name N or name CA or name C or name O or name CB \ )) or resid 660 through 664 or (resid 665 and (name N or name CA or name C or n \ ame O or name CB )) or resid 666 through 687 or (resid 688 and (name N or name C \ A or name C or name O or name CB )) or resid 689 through 691 or (resid 692 throu \ gh 693 and (name N or name CA or name C or name O or name CB )) or resid 694 thr \ ough 705 or (resid 706 and (name N or name CA or name C or name O or name CB )) \ or resid 707 through 708 or (resid 709 and (name N or name CA or name C or name \ O or name CB )) or resid 710 through 767 or resid 782 through 813 or (resid 814 \ through 815 and (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'E' and (resid 5 through 72 or (resid 73 and (name N or name CA or name C \ or name O or name CB )) or resid 74 through 94 or resid 96 through 209)) selection = (chain 'F' and (resid 5 through 72 or (resid 73 and (name N or name CA or name C \ or name O or name CB )) or resid 74 through 209)) selection = (chain 'G' and (resid 5 through 94 or resid 96 through 209)) selection = (chain 'H' and (resid 5 through 72 or (resid 73 and (name N or name CA or name C \ or name O or name CB )) or resid 74 through 94 or resid 96 through 209)) } 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=0.10 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 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: 4.510 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 50.560 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.080 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 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 : 0.012 0.072 17281 Z= 0.753 Angle : 1.426 23.378 23463 Z= 1.035 Chirality : 0.102 0.503 2712 Planarity : 0.011 0.200 2882 Dihedral : 15.167 81.533 5782 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.60 % Allowed : 2.54 % Favored : 96.86 % Rotamer: Outliers : 3.81 % Allowed : 16.62 % Favored : 79.57 % Cbeta Deviations : 0.49 % Peptide Plane: Cis-proline : 21.43 % 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: 0.03 (0.17), residues: 2185 helix: 0.91 (0.13), residues: 1307 sheet: -2.31 (0.36), residues: 156 loop : -0.98 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 601 HIS 0.006 0.002 HIS F 60 PHE 0.033 0.002 PHE B 663 TYR 0.022 0.003 TYR A 417 ARG 0.013 0.001 ARG C 416 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 247 time to evaluate : 2.081 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 795 LEU cc_start: 0.9355 (tp) cc_final: 0.9054 (tt) REVERT: C 484 VAL cc_start: -0.0665 (OUTLIER) cc_final: -0.1483 (p) REVERT: C 605 THR cc_start: 0.9020 (m) cc_final: 0.8555 (m) REVERT: C 611 SER cc_start: 0.9606 (m) cc_final: 0.9352 (p) REVERT: D 615 ASN cc_start: 0.8616 (t0) cc_final: 0.8175 (t0) REVERT: E 10 MET cc_start: 0.8443 (tpt) cc_final: 0.8023 (tpt) REVERT: E 81 ASP cc_start: 0.7525 (t0) cc_final: 0.7232 (t0) REVERT: E 97 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9233 (tt) REVERT: F 58 MET cc_start: 0.8325 (mmm) cc_final: 0.7834 (tpp) REVERT: G 136 LEU cc_start: 0.8866 (tp) cc_final: 0.8635 (pp) REVERT: H 81 ASP cc_start: 0.8173 (t0) cc_final: 0.7813 (t0) outliers start: 62 outliers final: 26 residues processed: 292 average time/residue: 0.2773 time to fit residues: 124.3031 Evaluate side-chains 195 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 167 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 638 GLN Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 726 LYS Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 499 MET Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 801 LEU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 144 SER Chi-restraints excluded: chain H residue 150 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 3.9990 chunk 166 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 172 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 128 optimal weight: 0.9990 chunk 199 optimal weight: 3.9990 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 431 HIS A 638 GLN C 583 GLN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 17281 Z= 0.180 Angle : 0.590 9.008 23463 Z= 0.305 Chirality : 0.040 0.242 2712 Planarity : 0.004 0.037 2882 Dihedral : 5.167 53.770 2461 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.48 % Favored : 98.29 % Rotamer: Outliers : 3.39 % Allowed : 18.88 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: 1.45 (0.18), residues: 2185 helix: 2.18 (0.14), residues: 1329 sheet: -2.03 (0.34), residues: 170 loop : -0.67 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 601 HIS 0.006 0.001 HIS F 60 PHE 0.019 0.001 PHE D 542 TYR 0.024 0.001 TYR C 420 ARG 0.006 0.000 ARG C 739 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 195 time to evaluate : 1.979 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 403 MET cc_start: 0.7040 (OUTLIER) cc_final: 0.6814 (mpp) REVERT: A 459 MET cc_start: 0.5799 (mpp) cc_final: 0.5450 (mpp) REVERT: A 538 LEU cc_start: 0.9412 (tp) cc_final: 0.9171 (tt) REVERT: A 795 LEU cc_start: 0.9420 (tp) cc_final: 0.9216 (tt) REVERT: C 605 THR cc_start: 0.8811 (m) cc_final: 0.8412 (m) REVERT: C 611 SER cc_start: 0.9568 (m) cc_final: 0.9328 (p) REVERT: C 704 MET cc_start: 0.7366 (mpp) cc_final: 0.6991 (mpp) REVERT: D 403 MET cc_start: 0.3152 (mpp) cc_final: 0.2834 (mpp) REVERT: E 37 ARG cc_start: 0.8052 (mtp85) cc_final: 0.7603 (mmm-85) REVERT: E 81 ASP cc_start: 0.7465 (t0) cc_final: 0.7132 (t0) REVERT: F 24 MET cc_start: 0.8790 (tpt) cc_final: 0.8117 (tpt) REVERT: F 58 MET cc_start: 0.8481 (mmm) cc_final: 0.8134 (tpp) REVERT: F 81 ASP cc_start: 0.8620 (t0) cc_final: 0.8403 (t0) REVERT: G 33 TRP cc_start: 0.7971 (m-10) cc_final: 0.7517 (m100) REVERT: G 58 MET cc_start: 0.8310 (tpp) cc_final: 0.7995 (tpp) REVERT: G 70 GLU cc_start: 0.8114 (mp0) cc_final: 0.7686 (mp0) REVERT: G 206 GLN cc_start: 0.9221 (pt0) cc_final: 0.8967 (pp30) REVERT: H 81 ASP cc_start: 0.8142 (t0) cc_final: 0.7729 (t0) outliers start: 55 outliers final: 28 residues processed: 233 average time/residue: 0.2508 time to fit residues: 93.2770 Evaluate side-chains 198 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 169 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 431 HIS Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 638 GLN Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 519 TYR Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain D residue 443 ASP Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 808 ILE Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 157 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 111 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 166 optimal weight: 9.9990 chunk 136 optimal weight: 7.9990 chunk 55 optimal weight: 0.0770 chunk 200 optimal weight: 1.9990 chunk 216 optimal weight: 9.9990 chunk 178 optimal weight: 0.9980 chunk 198 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 160 optimal weight: 10.0000 overall best weight: 3.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 583 GLN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 HIS ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17281 Z= 0.270 Angle : 0.620 9.321 23463 Z= 0.325 Chirality : 0.041 0.198 2712 Planarity : 0.004 0.042 2882 Dihedral : 4.533 51.970 2423 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.80 % Favored : 97.97 % Rotamer: Outliers : 4.11 % Allowed : 19.48 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: 1.63 (0.18), residues: 2185 helix: 2.25 (0.14), residues: 1332 sheet: -1.91 (0.33), residues: 202 loop : -0.34 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 601 HIS 0.028 0.002 HIS A 431 PHE 0.025 0.001 PHE C 655 TYR 0.019 0.002 TYR C 728 ARG 0.007 0.001 ARG A 481 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 165 time to evaluate : 2.007 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: B 581 MET cc_start: 0.8949 (mmp) cc_final: 0.8486 (mmm) REVERT: C 403 MET cc_start: 0.2520 (mpp) cc_final: 0.2053 (mpp) REVERT: C 500 ILE cc_start: 0.7478 (OUTLIER) cc_final: 0.7025 (mm) REVERT: C 605 THR cc_start: 0.8868 (m) cc_final: 0.8487 (m) REVERT: C 704 MET cc_start: 0.7499 (mpp) cc_final: 0.7134 (mpp) REVERT: E 81 ASP cc_start: 0.7475 (t0) cc_final: 0.7136 (t0) REVERT: E 190 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8327 (tm-30) REVERT: F 104 SER cc_start: 0.7996 (OUTLIER) cc_final: 0.7752 (p) REVERT: F 204 HIS cc_start: 0.5961 (OUTLIER) cc_final: 0.5701 (m170) REVERT: G 58 MET cc_start: 0.8321 (tpp) cc_final: 0.8074 (tpp) REVERT: G 70 GLU cc_start: 0.7981 (mp0) cc_final: 0.7730 (mp0) REVERT: G 81 ASP cc_start: 0.7955 (t0) cc_final: 0.7635 (t0) REVERT: G 190 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8161 (mm-30) REVERT: H 81 ASP cc_start: 0.7913 (t0) cc_final: 0.7449 (t0) outliers start: 67 outliers final: 39 residues processed: 216 average time/residue: 0.2739 time to fit residues: 94.8743 Evaluate side-chains 192 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 150 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain C residue 405 LYS Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 808 ILE Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 121 CYS Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 157 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 4.9990 chunk 150 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 22 optimal weight: 30.0000 chunk 95 optimal weight: 0.7980 chunk 134 optimal weight: 0.4980 chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 8.9990 chunk 104 optimal weight: 7.9990 chunk 190 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 HIS ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17281 Z= 0.167 Angle : 0.567 13.190 23463 Z= 0.284 Chirality : 0.040 0.173 2712 Planarity : 0.003 0.044 2882 Dihedral : 4.107 51.953 2420 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.48 % Favored : 98.29 % Rotamer: Outliers : 3.04 % Allowed : 22.04 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: 1.92 (0.18), residues: 2185 helix: 2.43 (0.14), residues: 1333 sheet: -1.57 (0.37), residues: 167 loop : -0.29 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 601 HIS 0.005 0.001 HIS A 431 PHE 0.015 0.001 PHE D 542 TYR 0.017 0.001 TYR C 728 ARG 0.005 0.000 ARG B 416 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 165 time to evaluate : 1.909 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 511 PHE cc_start: 0.5625 (OUTLIER) cc_final: 0.3942 (p90) REVERT: A 538 LEU cc_start: 0.9371 (tp) cc_final: 0.9155 (tt) REVERT: B 581 MET cc_start: 0.8993 (mmp) cc_final: 0.8609 (mmm) REVERT: B 686 MET cc_start: 0.6634 (tpp) cc_final: 0.6320 (tpp) REVERT: C 403 MET cc_start: 0.2281 (mpp) cc_final: 0.1693 (mpp) REVERT: C 405 LYS cc_start: 0.4648 (OUTLIER) cc_final: 0.4139 (pttm) REVERT: C 500 ILE cc_start: 0.7390 (OUTLIER) cc_final: 0.7068 (mm) REVERT: C 605 THR cc_start: 0.8786 (m) cc_final: 0.8417 (m) REVERT: C 704 MET cc_start: 0.7448 (mpp) cc_final: 0.7236 (mpp) REVERT: E 81 ASP cc_start: 0.7522 (t0) cc_final: 0.7190 (t0) REVERT: E 190 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8419 (tm-30) REVERT: F 24 MET cc_start: 0.8936 (tpt) cc_final: 0.8179 (tpt) REVERT: F 58 MET cc_start: 0.8360 (tpp) cc_final: 0.7916 (tpp) REVERT: F 81 ASP cc_start: 0.8340 (t0) cc_final: 0.8058 (t0) REVERT: G 66 THR cc_start: 0.8917 (OUTLIER) cc_final: 0.8650 (m) REVERT: G 190 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8260 (mm-30) REVERT: G 204 HIS cc_start: 0.5364 (OUTLIER) cc_final: 0.4353 (m-70) REVERT: H 10 MET cc_start: 0.8635 (ppp) cc_final: 0.8356 (ppp) REVERT: H 81 ASP cc_start: 0.7912 (t0) cc_final: 0.7417 (t0) REVERT: H 147 LEU cc_start: 0.9537 (mm) cc_final: 0.9292 (mt) outliers start: 51 outliers final: 31 residues processed: 201 average time/residue: 0.2463 time to fit residues: 80.1017 Evaluate side-chains 190 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 154 time to evaluate : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain C residue 405 LYS Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 519 TYR Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 799 LEU Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 523 MET Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 150 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 0.7980 chunk 120 optimal weight: 0.0870 chunk 3 optimal weight: 20.0000 chunk 158 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 181 optimal weight: 3.9990 chunk 146 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 108 optimal weight: 6.9990 chunk 190 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 overall best weight: 3.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 583 GLN D 743 ASN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 HIS ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17281 Z= 0.258 Angle : 0.606 10.728 23463 Z= 0.313 Chirality : 0.040 0.164 2712 Planarity : 0.004 0.051 2882 Dihedral : 4.202 49.522 2416 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.17 % Favored : 97.60 % Rotamer: Outliers : 4.11 % Allowed : 22.22 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: 1.74 (0.18), residues: 2185 helix: 2.25 (0.14), residues: 1334 sheet: -1.70 (0.39), residues: 155 loop : -0.29 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 601 HIS 0.006 0.001 HIS G 204 PHE 0.022 0.001 PHE C 654 TYR 0.019 0.001 TYR B 728 ARG 0.005 0.000 ARG A 481 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 159 time to evaluate : 1.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 MET cc_start: 0.6918 (mpp) cc_final: 0.6385 (mpp) REVERT: A 459 MET cc_start: 0.6724 (mpp) cc_final: 0.5885 (mpp) REVERT: A 511 PHE cc_start: 0.5443 (OUTLIER) cc_final: 0.3774 (p90) REVERT: B 686 MET cc_start: 0.6669 (tpp) cc_final: 0.6344 (tpp) REVERT: C 403 MET cc_start: 0.2469 (mpp) cc_final: 0.1847 (mpp) REVERT: C 405 LYS cc_start: 0.5034 (OUTLIER) cc_final: 0.4680 (mtmm) REVERT: C 459 MET cc_start: 0.6036 (mmp) cc_final: 0.5532 (mmp) REVERT: C 500 ILE cc_start: 0.7469 (OUTLIER) cc_final: 0.7176 (mm) REVERT: C 605 THR cc_start: 0.8848 (m) cc_final: 0.8500 (m) REVERT: D 470 VAL cc_start: 0.5019 (OUTLIER) cc_final: 0.4800 (t) REVERT: E 81 ASP cc_start: 0.7478 (t0) cc_final: 0.7168 (t0) REVERT: F 24 MET cc_start: 0.9153 (tpt) cc_final: 0.8895 (tpt) REVERT: F 58 MET cc_start: 0.8449 (tpp) cc_final: 0.7969 (tpp) REVERT: G 58 MET cc_start: 0.8202 (tpp) cc_final: 0.7962 (tpp) REVERT: G 70 GLU cc_start: 0.8187 (mp0) cc_final: 0.7614 (mp0) REVERT: G 81 ASP cc_start: 0.8235 (t0) cc_final: 0.7928 (t0) REVERT: G 190 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8322 (mm-30) REVERT: G 204 HIS cc_start: 0.5746 (OUTLIER) cc_final: 0.5458 (m-70) REVERT: H 10 MET cc_start: 0.8673 (ppp) cc_final: 0.8443 (ppp) REVERT: H 181 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.8018 (m-80) outliers start: 67 outliers final: 39 residues processed: 211 average time/residue: 0.2342 time to fit residues: 81.2370 Evaluate side-chains 193 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 148 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain C residue 405 LYS Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 519 TYR Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 583 GLN Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 799 LEU Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 523 MET Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 808 ILE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 181 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 7.9990 chunk 191 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 124 optimal weight: 20.0000 chunk 52 optimal weight: 2.9990 chunk 212 optimal weight: 5.9990 chunk 176 optimal weight: 8.9990 chunk 98 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 70 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 ASN G 204 HIS ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 17281 Z= 0.384 Angle : 0.726 16.255 23463 Z= 0.376 Chirality : 0.043 0.242 2712 Planarity : 0.004 0.053 2882 Dihedral : 4.656 46.154 2416 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 20.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.40 % Favored : 97.42 % Rotamer: Outliers : 4.71 % Allowed : 22.75 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: 1.15 (0.18), residues: 2185 helix: 1.71 (0.14), residues: 1330 sheet: -1.91 (0.42), residues: 140 loop : -0.41 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 601 HIS 0.008 0.001 HIS G 204 PHE 0.021 0.002 PHE C 491 TYR 0.021 0.002 TYR C 728 ARG 0.013 0.001 ARG F 74 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 142 time to evaluate : 1.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 MET cc_start: 0.7660 (mpp) cc_final: 0.6988 (mpp) REVERT: A 511 PHE cc_start: 0.4776 (OUTLIER) cc_final: 0.3713 (p90) REVERT: C 403 MET cc_start: 0.2330 (mpp) cc_final: 0.1826 (mpp) REVERT: C 500 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.7323 (mm) REVERT: C 704 MET cc_start: 0.6712 (mpp) cc_final: 0.6229 (mpp) REVERT: E 81 ASP cc_start: 0.7153 (t0) cc_final: 0.6816 (t0) REVERT: F 58 MET cc_start: 0.8544 (tpp) cc_final: 0.8122 (tpp) REVERT: G 70 GLU cc_start: 0.8310 (mp0) cc_final: 0.8077 (mp0) REVERT: G 81 ASP cc_start: 0.8426 (t0) cc_final: 0.8207 (t0) REVERT: G 190 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8540 (mm-30) REVERT: G 204 HIS cc_start: 0.5761 (OUTLIER) cc_final: 0.4787 (m90) REVERT: H 10 MET cc_start: 0.8693 (ppp) cc_final: 0.8477 (ppp) REVERT: H 117 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.7877 (t80) REVERT: H 181 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.8048 (m-80) outliers start: 77 outliers final: 53 residues processed: 206 average time/residue: 0.2350 time to fit residues: 79.7270 Evaluate side-chains 192 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 134 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain C residue 405 LYS Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 519 TYR Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 799 LEU Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 446 TYR Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 523 MET Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 808 ILE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 18 PHE Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 121 CYS Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 160 ASN Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 117 PHE Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 153 ILE Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 181 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 121 optimal weight: 30.0000 chunk 155 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 179 optimal weight: 8.9990 chunk 118 optimal weight: 20.0000 chunk 212 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 GLN C 582 GLN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 ASN G 204 HIS ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17281 Z= 0.203 Angle : 0.625 10.933 23463 Z= 0.314 Chirality : 0.040 0.168 2712 Planarity : 0.004 0.047 2882 Dihedral : 4.208 49.719 2414 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.80 % Favored : 98.02 % Rotamer: Outliers : 3.87 % Allowed : 23.59 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: 1.53 (0.18), residues: 2185 helix: 2.09 (0.14), residues: 1333 sheet: -2.13 (0.39), residues: 145 loop : -0.33 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 601 HIS 0.011 0.001 HIS G 204 PHE 0.019 0.001 PHE B 491 TYR 0.025 0.001 TYR B 728 ARG 0.010 0.000 ARG F 74 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 157 time to evaluate : 1.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 MET cc_start: 0.7106 (mpp) cc_final: 0.6321 (mpp) REVERT: A 511 PHE cc_start: 0.5398 (OUTLIER) cc_final: 0.3869 (p90) REVERT: A 538 LEU cc_start: 0.9373 (tp) cc_final: 0.9159 (tt) REVERT: A 582 GLN cc_start: 0.6934 (OUTLIER) cc_final: 0.6362 (tm130) REVERT: C 459 MET cc_start: 0.4917 (mmp) cc_final: 0.4493 (mmm) REVERT: C 500 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7386 (mm) REVERT: C 605 THR cc_start: 0.8761 (m) cc_final: 0.8409 (m) REVERT: C 704 MET cc_start: 0.6316 (mpp) cc_final: 0.5884 (mpp) REVERT: E 81 ASP cc_start: 0.7384 (t0) cc_final: 0.7090 (t0) REVERT: E 204 HIS cc_start: 0.7605 (OUTLIER) cc_final: 0.7253 (m170) REVERT: F 58 MET cc_start: 0.8539 (tpp) cc_final: 0.8123 (tpp) REVERT: G 58 MET cc_start: 0.8190 (tpp) cc_final: 0.7629 (tpp) REVERT: G 70 GLU cc_start: 0.8255 (mp0) cc_final: 0.7596 (mp0) REVERT: G 190 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8327 (mm-30) REVERT: G 204 HIS cc_start: 0.6436 (OUTLIER) cc_final: 0.5370 (m90) REVERT: H 10 MET cc_start: 0.8667 (ppp) cc_final: 0.8450 (ppp) REVERT: H 117 PHE cc_start: 0.8112 (OUTLIER) cc_final: 0.7790 (t80) REVERT: H 147 LEU cc_start: 0.9541 (mm) cc_final: 0.9307 (mt) REVERT: H 181 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.8038 (m-80) outliers start: 63 outliers final: 41 residues processed: 202 average time/residue: 0.2436 time to fit residues: 81.3697 Evaluate side-chains 194 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 146 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 582 GLN Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 704 MET Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 519 TYR Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 446 TYR Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 523 MET Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 121 CYS Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 160 ASN Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 117 PHE Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 181 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 0.2980 chunk 84 optimal weight: 7.9990 chunk 126 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 41 optimal weight: 30.0000 chunk 134 optimal weight: 2.9990 chunk 144 optimal weight: 30.0000 chunk 104 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 166 optimal weight: 7.9990 chunk 192 optimal weight: 20.0000 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 HIS G 204 HIS ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.4720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17281 Z= 0.273 Angle : 0.654 9.802 23463 Z= 0.333 Chirality : 0.041 0.170 2712 Planarity : 0.004 0.047 2882 Dihedral : 4.317 52.938 2414 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.54 % Favored : 97.28 % Rotamer: Outliers : 3.81 % Allowed : 24.12 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: 1.41 (0.18), residues: 2185 helix: 1.98 (0.14), residues: 1322 sheet: -1.83 (0.38), residues: 157 loop : -0.37 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 601 HIS 0.016 0.001 HIS G 204 PHE 0.015 0.001 PHE C 491 TYR 0.025 0.002 TYR B 643 ARG 0.009 0.000 ARG F 74 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 147 time to evaluate : 2.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 MET cc_start: 0.7176 (mpp) cc_final: 0.6592 (mpp) REVERT: A 459 MET cc_start: 0.7223 (mpp) cc_final: 0.6438 (mpp) REVERT: A 511 PHE cc_start: 0.4752 (OUTLIER) cc_final: 0.3714 (p90) REVERT: C 403 MET cc_start: 0.2734 (OUTLIER) cc_final: 0.2520 (mpp) REVERT: C 459 MET cc_start: 0.4926 (mmp) cc_final: 0.4664 (mmm) REVERT: C 500 ILE cc_start: 0.7932 (OUTLIER) cc_final: 0.7334 (mm) REVERT: C 605 THR cc_start: 0.8914 (m) cc_final: 0.8553 (m) REVERT: C 704 MET cc_start: 0.6239 (mpp) cc_final: 0.5733 (mpp) REVERT: E 81 ASP cc_start: 0.7358 (t0) cc_final: 0.7059 (t0) REVERT: F 24 MET cc_start: 0.9250 (tpt) cc_final: 0.8292 (tpt) REVERT: F 58 MET cc_start: 0.8545 (tpp) cc_final: 0.8144 (tpp) REVERT: G 58 MET cc_start: 0.8256 (tpp) cc_final: 0.7888 (tpp) REVERT: G 190 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8401 (mm-30) REVERT: G 204 HIS cc_start: 0.6259 (OUTLIER) cc_final: 0.5242 (m90) REVERT: H 10 MET cc_start: 0.8673 (ppp) cc_final: 0.8452 (ppp) REVERT: H 117 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7836 (t80) REVERT: H 181 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.8055 (m-80) outliers start: 62 outliers final: 49 residues processed: 195 average time/residue: 0.2281 time to fit residues: 73.4238 Evaluate side-chains 198 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 143 time to evaluate : 1.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 519 TYR Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 799 LEU Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 446 TYR Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 523 MET Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 742 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 808 ILE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 121 CYS Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 117 PHE Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 181 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 9.9990 chunk 185 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 118 optimal weight: 30.0000 chunk 86 optimal weight: 9.9990 chunk 155 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 178 optimal weight: 3.9990 chunk 186 optimal weight: 20.0000 chunk 196 optimal weight: 9.9990 chunk 129 optimal weight: 0.9980 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 GLN ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 582 GLN ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 ASN G 204 HIS ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 17281 Z= 0.289 Angle : 0.679 10.533 23463 Z= 0.347 Chirality : 0.041 0.179 2712 Planarity : 0.004 0.047 2882 Dihedral : 4.436 53.649 2414 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.40 % Favored : 97.42 % Rotamer: Outliers : 4.41 % Allowed : 23.70 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: 1.23 (0.18), residues: 2185 helix: 1.88 (0.14), residues: 1325 sheet: -1.93 (0.38), residues: 168 loop : -0.48 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 601 HIS 0.017 0.001 HIS G 204 PHE 0.015 0.001 PHE B 491 TYR 0.025 0.002 TYR B 728 ARG 0.009 0.000 ARG F 74 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 143 time to evaluate : 1.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 MET cc_start: 0.7162 (mpp) cc_final: 0.6360 (mpp) REVERT: A 511 PHE cc_start: 0.4789 (OUTLIER) cc_final: 0.3718 (p90) REVERT: A 601 TRP cc_start: 0.8466 (t-100) cc_final: 0.8232 (t-100) REVERT: A 717 MET cc_start: 0.8521 (pmm) cc_final: 0.8263 (pmm) REVERT: B 659 LYS cc_start: 0.7417 (OUTLIER) cc_final: 0.7030 (mptt) REVERT: C 403 MET cc_start: 0.2761 (OUTLIER) cc_final: 0.2397 (mpp) REVERT: C 459 MET cc_start: 0.5599 (mmp) cc_final: 0.5307 (mmm) REVERT: C 605 THR cc_start: 0.8771 (m) cc_final: 0.8432 (m) REVERT: C 670 MET cc_start: -0.2379 (ttt) cc_final: -0.2687 (ttt) REVERT: C 704 MET cc_start: 0.6390 (mpp) cc_final: 0.5975 (mpp) REVERT: E 81 ASP cc_start: 0.7265 (t0) cc_final: 0.6971 (t0) REVERT: F 24 MET cc_start: 0.9312 (tpt) cc_final: 0.8386 (tpt) REVERT: F 58 MET cc_start: 0.8568 (tpp) cc_final: 0.8168 (tpp) REVERT: G 190 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8488 (mm-30) REVERT: G 204 HIS cc_start: 0.6959 (OUTLIER) cc_final: 0.6318 (m90) REVERT: H 10 MET cc_start: 0.8656 (ppp) cc_final: 0.8415 (ppp) REVERT: H 117 PHE cc_start: 0.8111 (OUTLIER) cc_final: 0.7742 (t80) REVERT: H 181 PHE cc_start: 0.8637 (OUTLIER) cc_final: 0.8009 (m-80) outliers start: 72 outliers final: 53 residues processed: 200 average time/residue: 0.2374 time to fit residues: 78.1289 Evaluate side-chains 202 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 143 time to evaluate : 2.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 582 GLN Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 519 TYR Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 799 LEU Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 446 TYR Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 523 MET Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 742 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 808 ILE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 121 CYS Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 117 PHE Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 181 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 145 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 201 optimal weight: 6.9990 chunk 174 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 134 optimal weight: 0.6980 chunk 107 optimal weight: 9.9990 chunk 138 optimal weight: 7.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 HIS ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.4944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 17281 Z= 0.191 Angle : 0.652 14.825 23463 Z= 0.324 Chirality : 0.040 0.186 2712 Planarity : 0.004 0.047 2882 Dihedral : 4.312 56.997 2414 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.03 % Favored : 97.78 % Rotamer: Outliers : 3.16 % Allowed : 24.78 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: 1.49 (0.18), residues: 2185 helix: 2.07 (0.14), residues: 1326 sheet: -1.66 (0.41), residues: 150 loop : -0.45 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 601 HIS 0.025 0.001 HIS G 204 PHE 0.015 0.001 PHE B 491 TYR 0.020 0.001 TYR B 643 ARG 0.008 0.000 ARG F 74 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 155 time to evaluate : 1.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 MET cc_start: 0.6798 (mpp) cc_final: 0.5892 (mpp) REVERT: A 511 PHE cc_start: 0.4990 (OUTLIER) cc_final: 0.3615 (p90) REVERT: A 538 LEU cc_start: 0.9366 (tp) cc_final: 0.9160 (tt) REVERT: A 581 MET cc_start: 0.8059 (mpp) cc_final: 0.7821 (mtm) REVERT: A 717 MET cc_start: 0.8491 (pmm) cc_final: 0.8234 (pmm) REVERT: B 659 LYS cc_start: 0.7330 (OUTLIER) cc_final: 0.7093 (mptt) REVERT: C 403 MET cc_start: 0.2975 (OUTLIER) cc_final: 0.2622 (mpp) REVERT: C 459 MET cc_start: 0.5256 (mmp) cc_final: 0.4951 (mmm) REVERT: C 500 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7523 (mm) REVERT: C 605 THR cc_start: 0.8882 (m) cc_final: 0.8526 (m) REVERT: C 670 MET cc_start: -0.2501 (ttt) cc_final: -0.2786 (ttt) REVERT: C 704 MET cc_start: 0.6342 (mpp) cc_final: 0.5964 (mpp) REVERT: E 81 ASP cc_start: 0.7242 (t0) cc_final: 0.6973 (t0) REVERT: F 24 MET cc_start: 0.9206 (tpt) cc_final: 0.8195 (tpt) REVERT: F 58 MET cc_start: 0.8553 (tpp) cc_final: 0.8133 (tpp) REVERT: G 190 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8342 (mm-30) REVERT: H 10 MET cc_start: 0.8638 (ppp) cc_final: 0.8405 (ppp) REVERT: H 117 PHE cc_start: 0.8103 (OUTLIER) cc_final: 0.7743 (t80) REVERT: H 181 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.7990 (m-80) outliers start: 51 outliers final: 43 residues processed: 192 average time/residue: 0.2337 time to fit residues: 73.8786 Evaluate side-chains 198 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 149 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 519 TYR Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 523 MET Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 742 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 121 CYS Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 117 PHE Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 181 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 8.9990 chunk 53 optimal weight: 0.1980 chunk 160 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 174 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 179 optimal weight: 0.0020 chunk 22 optimal weight: 0.0770 chunk 32 optimal weight: 0.9990 chunk 153 optimal weight: 9.9990 overall best weight: 0.3948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 GLN ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.097777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.070290 restraints weight = 281201.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.072925 restraints weight = 116070.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.074547 restraints weight = 64533.420| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3683 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3683 r_free = 0.3683 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3683 r_free = 0.3683 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3683 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17281 Z= 0.164 Angle : 0.640 14.671 23463 Z= 0.315 Chirality : 0.040 0.177 2712 Planarity : 0.004 0.046 2882 Dihedral : 4.102 54.890 2414 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.52 % Favored : 98.29 % Rotamer: Outliers : 2.26 % Allowed : 25.67 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: 1.66 (0.18), residues: 2185 helix: 2.17 (0.14), residues: 1335 sheet: -1.65 (0.44), residues: 128 loop : -0.40 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 601 HIS 0.005 0.001 HIS H 204 PHE 0.032 0.001 PHE C 580 TYR 0.020 0.001 TYR B 643 ARG 0.008 0.000 ARG F 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3078.57 seconds wall clock time: 57 minutes 37.80 seconds (3457.80 seconds total)