Starting phenix.real_space_refine on Sun Mar 17 06:24:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3v_17396/03_2024/8p3v_17396.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3v_17396/03_2024/8p3v_17396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3v_17396/03_2024/8p3v_17396.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3v_17396/03_2024/8p3v_17396.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3v_17396/03_2024/8p3v_17396.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3v_17396/03_2024/8p3v_17396.pdb" } resolution = 3.53 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= 0.044 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 97 5.16 5 C 11085 2.51 5 N 2747 2.21 5 O 2985 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 624": "NH1" <-> "NH2" 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 PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 520": "OE1" <-> "OE2" Residue "C GLU 566": "OE1" <-> "OE2" Residue "C GLU 701": "OE1" <-> "OE2" 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 ARG 690": "NH1" <-> "NH2" Residue "D GLU 701": "OE1" <-> "OE2" Residue "E GLU 56": "OE1" <-> "OE2" Residue "F GLU 190": "OE1" <-> "OE2" Residue "G GLU 95": "OE1" <-> "OE2" Residue "G GLU 202": "OE1" <-> "OE2" Residue "H GLU 95": "OE1" <-> "OE2" Residue "H GLU 202": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16914 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 2862 Classifications: {'peptide': 392} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 377} Chain breaks: 3 Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 284 Unresolved non-hydrogen dihedrals: 204 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 6, 'GLU:plan': 14, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 148 Chain: "B" Number of atoms: 2912 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 384, 2881 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 371} Chain breaks: 4 Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 126 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': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 90 Conformer: "B" Number of residues, atoms: 384, 2881 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 371} Chain breaks: 4 Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 126 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': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 90 bond proxies already assigned to first conformer: 2909 Chain: "C" Number of atoms: 2859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 2859 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 373} Chain breaks: 4 Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 173 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': 3} Unresolved non-hydrogen planarities: 115 Chain: "D" Number of atoms: 2859 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 381, 2828 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 368} 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, 2828 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 368} 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: 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: "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=0.48 ... (20 atoms not shown) pdb=" CZ BPHE B 570 " occ=0.52 residue: pdb=" N AGLN B 582 " occ=0.35 ... (16 atoms not shown) pdb=" NE2BGLN B 582 " occ=0.65 residue: pdb=" N APHE B 619 " occ=0.34 ... (20 atoms not shown) pdb=" CZ BPHE B 619 " occ=0.66 residue: pdb=" N APHE D 570 " occ=0.63 ... (20 atoms not shown) pdb=" CZ BPHE D 570 " occ=0.37 residue: pdb=" N AGLN D 582 " occ=0.46 ... (16 atoms not shown) pdb=" NE2BGLN D 582 " occ=0.54 residue: pdb=" N APHE D 619 " occ=0.43 ... (20 atoms not shown) pdb=" CZ BPHE D 619 " occ=0.57 Time building chain proxies: 11.60, per 1000 atoms: 0.69 Number of scatterers: 16914 At special positions: 0 Unit cell: (117.925, 112.625, 137.8, 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 97 16.00 O 2985 8.00 N 2747 7.00 C 11085 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=2.01 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.04 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.03 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=2.03 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: 6.43 Conformation dependent library (CDL) restraints added in 4.2 seconds 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4114 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 27 sheets defined 61.9% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 407 through 411 removed outlier: 3.540A pdb=" N GLN A 410 " --> pdb=" O ASN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 415 removed outlier: 4.087A 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 Processing helix chain 'A' and resid 568 through 581 Processing helix chain 'A' and resid 591 through 623 removed outlier: 3.562A pdb=" N VAL A 597 " --> pdb=" O SER A 593 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU A 623 " --> pdb=" O PHE A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 636 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 815 removed outlier: 3.803A pdb=" N PHE A 792 " --> pdb=" O VAL A 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 411 removed outlier: 3.629A 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 511 through 515 Processing helix chain 'B' and resid 518 through 542 Processing helix chain 'B' and resid 568 through 581 Processing helix chain 'B' and resid 591 through 625 removed outlier: 3.910A pdb=" N GLU B 623 " --> pdb=" O APHE B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 638 Processing helix chain 'B' and resid 649 through 657 Processing helix chain 'B' and resid 660 through 673 removed outlier: 3.532A 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 788 through 815 removed outlier: 3.648A pdb=" N PHE B 792 " --> pdb=" O VAL B 788 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG B 815 " --> pdb=" O CYS B 811 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 411 removed outlier: 3.539A pdb=" N GLN C 410 " --> pdb=" O ASN C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 415 removed outlier: 4.290A 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: 3.854A pdb=" N LEU C 514 " --> pdb=" O PHE C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 542 Processing helix chain 'C' and resid 568 through 581 Processing helix chain 'C' and resid 591 through 623 removed outlier: 3.743A pdb=" N GLU C 623 " --> pdb=" O PHE C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 638 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: 3.742A pdb=" N PHE C 792 " --> pdb=" O VAL C 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 411 removed outlier: 3.564A pdb=" N GLN D 410 " --> pdb=" O ASN D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 415 removed outlier: 4.238A 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 Processing helix chain 'D' and resid 518 through 542 Processing helix chain 'D' and resid 568 through 581 Processing helix chain 'D' and resid 591 through 622 removed outlier: 3.543A pdb=" N VAL D 597 " --> pdb=" O SER D 593 " (cutoff:3.500A) 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: 3.735A 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: 4.184A pdb=" N GLU E 126 " --> pdb=" O VAL E 122 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE E 127 " --> pdb=" O ALA E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 162 removed outlier: 3.702A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 209 Processing helix chain 'F' and resid 6 through 30 removed outlier: 3.524A pdb=" N MET F 10 " --> pdb=" O ARG F 6 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU F 11 " --> pdb=" O GLY F 7 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 105 removed outlier: 3.608A pdb=" N LEU F 97 " --> pdb=" O THR F 93 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 125 Processing helix chain 'F' and resid 133 through 162 Processing helix chain 'F' and resid 176 through 209 removed outlier: 3.986A pdb=" N LEU F 207 " --> pdb=" O LYS F 203 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA F 209 " --> pdb=" O GLN F 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 30 removed outlier: 3.765A pdb=" N THR G 13 " --> pdb=" O GLN G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 105 Processing helix chain 'G' and resid 105 through 128 removed outlier: 3.889A pdb=" N GLU G 126 " --> pdb=" O VAL G 122 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 162 removed outlier: 3.888A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 209 removed outlier: 3.614A 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: 3.790A pdb=" N GLU H 126 " --> pdb=" O VAL H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 162 removed outlier: 3.871A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 209 Processing sheet with id=AA1, first strand: chain 'A' and resid 436 through 440 removed outlier: 6.618A pdb=" N TYR A 391 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLU A 439 " --> pdb=" O TYR A 391 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N VAL A 393 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 470 " --> pdb=" O ILE A 392 " (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: 3.675A 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: 4.054A pdb=" N MET A 492 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 700 through 701 removed outlier: 4.169A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 643 through 644 Processing sheet with id=AA8, first strand: chain 'B' and resid 436 through 440 removed outlier: 6.699A pdb=" N TYR B 391 " --> pdb=" O ARG B 437 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLU B 439 " --> pdb=" O TYR B 391 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N VAL B 393 " --> pdb=" O GLU B 439 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL B 470 " --> pdb=" O ILE B 392 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 403 through 404 Processing sheet with id=AB1, first strand: chain 'B' and resid 485 through 487 Processing sheet with id=AB2, first strand: chain 'B' and resid 492 through 494 removed outlier: 3.904A pdb=" N MET B 492 " --> pdb=" O TYR B 728 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 642 through 644 removed outlier: 6.470A pdb=" N ALA B 642 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 7.576A 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: 8.842A pdb=" N GLU B 701 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE B 498 " --> pdb=" O VAL B 719 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 436 through 440 removed outlier: 6.566A pdb=" N TYR C 391 " --> pdb=" O ARG C 437 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLU C 439 " --> pdb=" O TYR C 391 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N VAL C 393 " --> pdb=" O GLU C 439 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 403 through 404 Processing sheet with id=AB6, first strand: chain 'C' and resid 447 through 450 removed outlier: 3.780A pdb=" N ALA C 448 " --> pdb=" O ASN C 457 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA C 455 " --> pdb=" O ASP C 450 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 485 through 487 Processing sheet with id=AB8, first strand: chain 'C' and resid 492 through 494 removed outlier: 3.870A pdb=" N MET C 492 " --> pdb=" O TYR C 728 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 642 through 644 removed outlier: 6.553A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR C 698 " --> pdb=" O MET C 499 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 436 through 440 removed outlier: 6.367A pdb=" N TYR D 391 " --> pdb=" O ARG D 437 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLU D 439 " --> pdb=" O TYR D 391 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N VAL D 393 " --> pdb=" O GLU D 439 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL D 470 " --> pdb=" O ILE D 392 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 403 through 404 Processing sheet with id=AC3, first strand: chain 'D' and resid 485 through 487 Processing sheet with id=AC4, first strand: chain 'D' and resid 492 through 494 removed outlier: 3.828A pdb=" N MET D 492 " --> pdb=" O TYR D 728 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 642 through 644 removed outlier: 6.597A pdb=" N ALA D 642 " --> pdb=" O ALA D 697 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N LEU D 699 " --> pdb=" O ALA D 642 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLY D 644 " --> pdb=" O LEU D 699 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N GLU D 701 " --> pdb=" O GLY D 644 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE D 498 " --> pdb=" O VAL D 719 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 77 through 79 removed outlier: 3.637A pdb=" N LYS E 78 " --> pdb=" O THR E 66 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 77 through 79 Processing sheet with id=AC8, first strand: chain 'G' and resid 77 through 79 Processing sheet with id=AC9, first strand: chain 'H' and resid 77 through 79 removed outlier: 4.057A pdb=" N LYS H 78 " --> pdb=" O THR H 66 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR H 66 " --> pdb=" O LYS H 78 " (cutoff:3.500A) 1126 hydrogen bonds defined for protein. 3266 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.58 Time building geometry restraints manager: 7.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3330 1.32 - 1.45: 4294 1.45 - 1.58: 9526 1.58 - 1.70: 0 1.70 - 1.83: 158 Bond restraints: 17308 Sorted by residual: bond pdb=" C ILE D 641 " pdb=" O ILE D 641 " ideal model delta sigma weight residual 1.234 1.290 -0.056 1.17e-02 7.31e+03 2.32e+01 bond pdb=" C TYR D 391 " pdb=" O TYR D 391 " ideal model delta sigma weight residual 1.234 1.293 -0.060 1.34e-02 5.57e+03 1.98e+01 bond pdb=" N VAL C 484 " pdb=" CA VAL C 484 " ideal model delta sigma weight residual 1.456 1.498 -0.041 9.50e-03 1.11e+04 1.88e+01 bond pdb=" N VAL A 484 " pdb=" CA VAL A 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 SER D 631 " pdb=" O SER D 631 " ideal model delta sigma weight residual 1.235 1.275 -0.040 1.00e-02 1.00e+04 1.59e+01 ... (remaining 17303 not shown) Histogram of bond angle deviations from ideal: 93.13 - 101.82: 74 101.82 - 110.50: 4861 110.50 - 119.19: 10160 119.19 - 127.88: 8281 127.88 - 136.56: 128 Bond angle restraints: 23504 Sorted by residual: angle pdb=" O GLU C 623 " pdb=" C GLU C 623 " pdb=" N ARG C 624 " ideal model delta sigma weight residual 122.59 136.56 -13.97 1.33e+00 5.65e-01 1.10e+02 angle pdb=" CA PRO D 508 " pdb=" N PRO D 508 " pdb=" CD PRO D 508 " ideal model delta sigma weight residual 112.00 99.47 12.53 1.40e+00 5.10e-01 8.01e+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 93.13 17.29 1.99e+00 2.53e-01 7.55e+01 angle pdb=" C GLU C 623 " pdb=" N ARG C 624 " pdb=" CA ARG C 624 " ideal model delta sigma weight residual 121.70 107.20 14.50 1.80e+00 3.09e-01 6.49e+01 angle pdb=" C ILE D 498 " pdb=" CA ILE D 498 " pdb=" CB ILE D 498 " ideal model delta sigma weight residual 110.82 100.36 10.46 1.54e+00 4.22e-01 4.61e+01 ... (remaining 23499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 8752 17.96 - 35.93: 909 35.93 - 53.89: 211 53.89 - 71.85: 45 71.85 - 89.82: 11 Dihedral angle restraints: 9928 sinusoidal: 3484 harmonic: 6444 Sorted by residual: 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 -105.64 -16.96 0 2.50e+00 1.60e-01 4.60e+01 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 36.71 56.29 1 1.00e+01 1.00e-02 4.27e+01 dihedral pdb=" CB CYS H 67 " pdb=" SG CYS H 67 " pdb=" SG CYS H 77 " pdb=" CB CYS H 77 " ideal model delta sinusoidal sigma weight residual 93.00 46.49 46.51 1 1.00e+01 1.00e-02 2.99e+01 ... (remaining 9925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1570 0.084 - 0.169: 998 0.169 - 0.253: 132 0.253 - 0.338: 11 0.338 - 0.422: 4 Chirality restraints: 2715 Sorted by residual: chirality pdb=" CG LEU D 635 " pdb=" CB LEU D 635 " pdb=" CD1 LEU D 635 " pdb=" CD2 LEU D 635 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" CB VAL A 742 " pdb=" CA VAL A 742 " pdb=" CG1 VAL A 742 " pdb=" CG2 VAL A 742 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" CA ILE D 500 " pdb=" N ILE D 500 " pdb=" C ILE D 500 " pdb=" CB ILE D 500 " both_signs ideal model delta sigma weight residual False 2.43 2.82 -0.39 2.00e-01 2.50e+01 3.75e+00 ... (remaining 2712 not shown) Planarity restraints: 2893 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 624 " -0.562 9.50e-02 1.11e+02 2.52e-01 3.87e+01 pdb=" NE ARG A 624 " 0.033 2.00e-02 2.50e+03 pdb=" CZ ARG A 624 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A 624 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 624 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 711 " 0.416 9.50e-02 1.11e+02 1.87e-01 2.14e+01 pdb=" NE ARG A 711 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG A 711 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 711 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 711 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 657 " -0.370 9.50e-02 1.11e+02 1.66e-01 1.69e+01 pdb=" NE ARG A 657 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG A 657 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 657 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 657 " -0.015 2.00e-02 2.50e+03 ... (remaining 2890 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4066 2.79 - 3.32: 17054 3.32 - 3.84: 27979 3.84 - 4.37: 32523 4.37 - 4.90: 56144 Nonbonded interactions: 137766 Sorted by model distance: nonbonded pdb=" OG1 THR F 30 " pdb=" OG SER F 178 " model vdw 2.259 2.440 nonbonded pdb=" O SER C 631 " pdb=" OD1 ASP C 634 " model vdw 2.302 3.040 nonbonded pdb=" O ILE E 154 " pdb=" OG SER E 158 " model vdw 2.304 2.440 nonbonded pdb=" O SER E 36 " pdb=" OG1 THR E 59 " model vdw 2.305 2.440 nonbonded pdb=" OG SER G 125 " pdb=" OE2 GLU G 126 " model vdw 2.309 2.440 ... (remaining 137761 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 623 or resid 631 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 502 or resid 509 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 622 or (resid 623 and (name N or name CA or name C or name O or name CB \ )) or resid 631 through 632 or (resid 633 through 638 and (name N or name CA or \ name C or name O or name CB )) or resid 639 through 640 or (resid 641 through 6 \ 43 and (name N or name CA or name C or name O or name CB )) or resid 644 through \ 658 or (resid 659 and (name N or name CA or name C or name O or name CB )) or r \ esid 660 through 664 or (resid 665 and (name N or name CA or name C or name O or \ name CB )) or resid 666 through 683 or (resid 684 and (name N or name CA or nam \ e C or name O or name CB )) or resid 685 through 687 or (resid 688 and (name N o \ r name CA or name C or name O or name CB )) or resid 689 through 690 or (resid 6 \ 91 through 693 and (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 nam \ e 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 623 or resid 631 t \ hrough 633 or (resid 634 through 638 and (name N or name CA or name C or name O \ or name CB )) or resid 639 through 640 or (resid 641 through 643 and (name N or \ name CA or name C or name O or name CB )) or resid 644 through 687 or (resid 688 \ and (name N or name CA or name C or name O or name CB )) or resid 689 through 6 \ 91 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 through 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 50 \ 2 or resid 509 through 545 or (resid 566 and (name N or name CA or name C or nam \ e O or name CB )) or resid 567 through 569 or resid 571 through 581 or resid 583 \ through 618 or resid 620 through 634 or (resid 635 through 638 and (name N or n \ ame CA or name C or name O or name CB )) or resid 639 through 640 or (resid 641 \ through 643 and (name N or name CA or name C or name O or name CB )) or resid 64 \ 4 through 658 or (resid 659 and (name N or name CA or name C or name O or name C \ B )) or resid 660 through 664 or (resid 665 and (name N or name CA or name C or \ name O or name CB )) or resid 666 through 687 or (resid 688 and (name N or name \ CA or name C or name O or name CB )) or resid 689 through 691 or (resid 692 thro \ ugh 693 and (name N or name CA or name C or name O or name CB )) or resid 694 th \ rough 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 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' 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 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=0.34 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: 1.000 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: 4.640 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 49.570 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 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 : 0.011 0.075 17308 Z= 0.732 Angle : 1.331 17.288 23504 Z= 0.964 Chirality : 0.096 0.422 2715 Planarity : 0.012 0.252 2893 Dihedral : 15.532 89.818 5790 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.55 % Allowed : 2.89 % Favored : 96.55 % Rotamer: Outliers : 5.25 % Allowed : 17.29 % Favored : 77.46 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 21.05 % 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: 0.15 (0.17), residues: 2195 helix: 1.09 (0.13), residues: 1317 sheet: -2.24 (0.38), residues: 137 loop : -1.16 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP D 456 HIS 0.008 0.002 HIS F 82 PHE 0.022 0.002 PHE B 678 TYR 0.021 0.004 TYR D 669 ARG 0.013 0.001 ARG A 690 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 209 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 ASP cc_start: 0.9275 (m-30) cc_final: 0.8846 (m-30) REVERT: B 443 ASP cc_start: 0.4226 (m-30) cc_final: 0.3962 (t0) REVERT: B 525 ILE cc_start: 0.9515 (mt) cc_final: 0.9251 (mp) REVERT: B 787 ASN cc_start: 0.8740 (OUTLIER) cc_final: 0.8417 (p0) REVERT: C 515 ASP cc_start: 0.9238 (m-30) cc_final: 0.9014 (m-30) REVERT: C 605 THR cc_start: 0.9675 (m) cc_final: 0.9442 (m) REVERT: C 657 ARG cc_start: 0.7326 (ptp-110) cc_final: 0.7075 (ptt-90) REVERT: D 670 MET cc_start: 0.2708 (mtt) cc_final: 0.1308 (mtm) REVERT: E 10 MET cc_start: 0.9317 (OUTLIER) cc_final: 0.8184 (tmm) REVERT: E 39 VAL cc_start: 0.9219 (OUTLIER) cc_final: 0.8942 (t) REVERT: E 58 MET cc_start: 0.8660 (tpt) cc_final: 0.8165 (tpt) REVERT: E 78 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8802 (ptpp) REVERT: F 203 LYS cc_start: 0.8957 (tppt) cc_final: 0.8735 (tppt) REVERT: F 204 HIS cc_start: 0.6899 (OUTLIER) cc_final: 0.5495 (m-70) REVERT: F 205 GLN cc_start: 0.9097 (tp40) cc_final: 0.8751 (pp30) REVERT: G 9 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8114 (tm130) REVERT: G 79 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7973 (mmtp) REVERT: G 102 ARG cc_start: 0.9297 (OUTLIER) cc_final: 0.8127 (tpt-90) REVERT: G 205 GLN cc_start: 0.8979 (mm-40) cc_final: 0.8123 (tm-30) REVERT: H 9 GLN cc_start: 0.9281 (mt0) cc_final: 0.8858 (mt0) REVERT: H 13 THR cc_start: 0.9548 (m) cc_final: 0.9300 (p) REVERT: H 24 MET cc_start: 0.8901 (tpp) cc_final: 0.8440 (tpp) REVERT: H 200 TYR cc_start: 0.9082 (t80) cc_final: 0.8876 (t80) outliers start: 87 outliers final: 49 residues processed: 280 average time/residue: 0.3112 time to fit residues: 127.2554 Evaluate side-chains 211 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 154 time to evaluate : 1.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain C residue 499 MET Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 637 LYS Chi-restraints excluded: chain C residue 734 LYS Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 781 SER Chi-restraints excluded: chain D residue 812 TYR Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 9 GLN Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 79 LYS Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 201 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 0.9990 chunk 167 optimal weight: 0.5980 chunk 92 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 173 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 chunk 128 optimal weight: 0.7980 chunk 200 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 9 GLN F 160 ASN G 204 HIS H 9 GLN ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 204 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 17308 Z= 0.177 Angle : 0.566 9.891 23504 Z= 0.297 Chirality : 0.039 0.153 2715 Planarity : 0.004 0.039 2893 Dihedral : 6.263 77.160 2525 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.06 % Favored : 98.85 % Rotamer: Outliers : 2.98 % Allowed : 19.26 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % 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: 2195 helix: 2.39 (0.14), residues: 1362 sheet: -1.56 (0.38), residues: 149 loop : -0.98 (0.21), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 574 HIS 0.004 0.001 HIS F 82 PHE 0.021 0.001 PHE D 655 TYR 0.021 0.001 TYR C 698 ARG 0.007 0.001 ARG H 65 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 174 time to evaluate : 1.944 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 515 ASP cc_start: 0.9276 (m-30) cc_final: 0.8692 (m-30) REVERT: A 520 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8486 (mp0) REVERT: A 581 MET cc_start: 0.9202 (OUTLIER) cc_final: 0.8679 (mpt) REVERT: A 587 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8606 (pp) REVERT: A 717 MET cc_start: 0.8790 (ppp) cc_final: 0.8309 (ppp) REVERT: B 403 MET cc_start: 0.2701 (mpp) cc_final: 0.1966 (mpp) REVERT: B 443 ASP cc_start: 0.3587 (m-30) cc_final: 0.3319 (t0) REVERT: B 459 MET cc_start: 0.4213 (mpp) cc_final: 0.3135 (ttp) REVERT: B 525 ILE cc_start: 0.9508 (mt) cc_final: 0.9222 (mp) REVERT: B 659 LYS cc_start: 0.6532 (mmtt) cc_final: 0.6247 (mmtt) REVERT: B 787 ASN cc_start: 0.8545 (OUTLIER) cc_final: 0.8252 (p0) REVERT: C 500 ILE cc_start: 0.6495 (OUTLIER) cc_final: 0.6277 (tp) REVERT: C 515 ASP cc_start: 0.9188 (m-30) cc_final: 0.8984 (m-30) REVERT: C 605 THR cc_start: 0.9373 (m) cc_final: 0.9126 (m) REVERT: C 657 ARG cc_start: 0.7448 (ptp-110) cc_final: 0.7062 (ptt90) REVERT: D 499 MET cc_start: 0.0735 (ppp) cc_final: 0.0489 (ppp) REVERT: F 56 GLU cc_start: 0.8677 (pm20) cc_final: 0.8453 (pm20) REVERT: F 203 LYS cc_start: 0.8974 (tppt) cc_final: 0.8756 (tppt) REVERT: F 208 ARG cc_start: 0.8409 (mpt180) cc_final: 0.8119 (ttp-170) REVERT: G 205 GLN cc_start: 0.9121 (mm-40) cc_final: 0.8451 (tm-30) REVERT: H 24 MET cc_start: 0.8976 (tpp) cc_final: 0.8392 (tpp) outliers start: 49 outliers final: 15 residues processed: 210 average time/residue: 0.2998 time to fit residues: 94.3397 Evaluate side-chains 168 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 148 time to evaluate : 1.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 173 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 111 optimal weight: 30.0000 chunk 62 optimal weight: 30.0000 chunk 167 optimal weight: 3.9990 chunk 136 optimal weight: 20.0000 chunk 55 optimal weight: 3.9990 chunk 201 optimal weight: 5.9990 chunk 217 optimal weight: 5.9990 chunk 179 optimal weight: 6.9990 chunk 199 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 ASN B 582 GLN A ** C 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN E 205 GLN ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 GLN ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 204 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 17308 Z= 0.408 Angle : 0.618 9.220 23504 Z= 0.330 Chirality : 0.041 0.143 2715 Planarity : 0.004 0.038 2893 Dihedral : 4.509 55.890 2433 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.88 % Favored : 98.07 % Rotamer: Outliers : 4.05 % Allowed : 20.39 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.18), residues: 2195 helix: 2.46 (0.14), residues: 1370 sheet: -1.35 (0.42), residues: 146 loop : -0.74 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 762 HIS 0.005 0.001 HIS G 204 PHE 0.015 0.002 PHE C 491 TYR 0.018 0.002 TYR B 812 ARG 0.004 0.001 ARG C 690 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 144 time to evaluate : 1.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 ASP cc_start: 0.9220 (m-30) cc_final: 0.8626 (m-30) REVERT: A 581 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.8547 (mpt) REVERT: A 587 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8617 (pp) REVERT: A 666 MET cc_start: 0.7852 (tpp) cc_final: 0.7645 (tpt) REVERT: A 717 MET cc_start: 0.9175 (ppp) cc_final: 0.8823 (ppp) REVERT: B 443 ASP cc_start: 0.4035 (m-30) cc_final: 0.3472 (t0) REVERT: B 459 MET cc_start: 0.4255 (mpp) cc_final: 0.3286 (ttp) REVERT: B 525 ILE cc_start: 0.9444 (mt) cc_final: 0.9165 (mp) REVERT: C 492 MET cc_start: 0.2008 (mmm) cc_final: 0.1789 (mmm) REVERT: C 515 ASP cc_start: 0.9192 (m-30) cc_final: 0.8958 (m-30) REVERT: C 582 GLN cc_start: 0.9475 (mt0) cc_final: 0.9191 (mt0) REVERT: C 605 THR cc_start: 0.9631 (m) cc_final: 0.9409 (p) REVERT: C 657 ARG cc_start: 0.7650 (ptp-110) cc_final: 0.7168 (ptt90) REVERT: C 801 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9257 (tp) REVERT: D 643 TYR cc_start: 0.2191 (OUTLIER) cc_final: 0.1968 (p90) REVERT: F 208 ARG cc_start: 0.8388 (mpt180) cc_final: 0.8002 (ttp80) REVERT: G 74 ARG cc_start: 0.8858 (ttp80) cc_final: 0.8557 (ttm110) REVERT: G 153 ILE cc_start: 0.9428 (OUTLIER) cc_final: 0.9108 (mp) REVERT: G 205 GLN cc_start: 0.9073 (mm-40) cc_final: 0.8503 (tm-30) REVERT: H 13 THR cc_start: 0.9399 (OUTLIER) cc_final: 0.9137 (p) REVERT: H 58 MET cc_start: 0.8680 (tpp) cc_final: 0.8417 (tpp) outliers start: 66 outliers final: 35 residues processed: 191 average time/residue: 0.2867 time to fit residues: 83.0092 Evaluate side-chains 182 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 141 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 414 ASN Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 756 ASP Chi-restraints excluded: chain C residue 801 LEU Chi-restraints excluded: chain D residue 489 LYS Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 643 TYR Chi-restraints excluded: chain D residue 704 MET Chi-restraints excluded: chain D residue 808 ILE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 150 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 198 optimal weight: 0.8980 chunk 151 optimal weight: 0.9990 chunk 104 optimal weight: 30.0000 chunk 22 optimal weight: 40.0000 chunk 95 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 201 optimal weight: 0.5980 chunk 213 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 191 optimal weight: 8.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN F 9 GLN ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 204 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 17308 Z= 0.157 Angle : 0.509 10.816 23504 Z= 0.263 Chirality : 0.038 0.186 2715 Planarity : 0.003 0.040 2893 Dihedral : 4.092 54.706 2429 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.22 % Allowed : 20.45 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.18), residues: 2195 helix: 2.79 (0.14), residues: 1370 sheet: -1.31 (0.39), residues: 157 loop : -0.60 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 574 HIS 0.003 0.001 HIS F 82 PHE 0.009 0.001 PHE F 179 TYR 0.013 0.001 TYR H 200 ARG 0.004 0.000 ARG G 37 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 155 time to evaluate : 1.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 520 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8511 (mp0) REVERT: A 581 MET cc_start: 0.9200 (OUTLIER) cc_final: 0.8718 (mpt) REVERT: A 587 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8604 (pp) REVERT: A 666 MET cc_start: 0.7921 (tpp) cc_final: 0.7633 (tpp) REVERT: A 717 MET cc_start: 0.9118 (ppp) cc_final: 0.8824 (ppp) REVERT: B 403 MET cc_start: 0.2954 (mpp) cc_final: 0.2704 (mpp) REVERT: B 443 ASP cc_start: 0.3891 (m-30) cc_final: 0.3422 (t0) REVERT: B 459 MET cc_start: 0.4071 (mpp) cc_final: 0.3386 (ttp) REVERT: B 492 MET cc_start: 0.0770 (mpp) cc_final: 0.0512 (mpp) REVERT: B 525 ILE cc_start: 0.9439 (mt) cc_final: 0.9151 (mp) REVERT: C 657 ARG cc_start: 0.7752 (ptp-110) cc_final: 0.7301 (ptt90) REVERT: C 686 MET cc_start: 0.8447 (tmm) cc_final: 0.8174 (tmm) REVERT: C 801 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9103 (tm) REVERT: D 581 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8653 (mmm) REVERT: E 160 ASN cc_start: 0.7896 (m-40) cc_final: 0.7689 (m110) REVERT: F 56 GLU cc_start: 0.8831 (pm20) cc_final: 0.8614 (pm20) REVERT: F 204 HIS cc_start: 0.6452 (OUTLIER) cc_final: 0.5737 (m-70) REVERT: F 208 ARG cc_start: 0.8292 (mpt180) cc_final: 0.8064 (ttp80) REVERT: G 153 ILE cc_start: 0.9385 (OUTLIER) cc_final: 0.9029 (mp) REVERT: G 202 GLU cc_start: 0.9159 (tm-30) cc_final: 0.8947 (tm-30) REVERT: G 205 GLN cc_start: 0.9073 (mm-40) cc_final: 0.8505 (tm-30) outliers start: 52 outliers final: 26 residues processed: 195 average time/residue: 0.2966 time to fit residues: 87.9259 Evaluate side-chains 177 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 144 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 801 LEU Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 808 ILE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 177 optimal weight: 7.9990 chunk 121 optimal weight: 50.0000 chunk 3 optimal weight: 5.9990 chunk 159 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 182 optimal weight: 0.9980 chunk 147 optimal weight: 30.0000 chunk 0 optimal weight: 40.0000 chunk 109 optimal weight: 0.8980 chunk 191 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 HIS ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 752 GLN ** C 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 204 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17308 Z= 0.286 Angle : 0.551 8.879 23504 Z= 0.287 Chirality : 0.039 0.174 2715 Planarity : 0.003 0.040 2893 Dihedral : 4.040 56.071 2429 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.82 % Allowed : 20.27 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.18), residues: 2195 helix: 2.76 (0.14), residues: 1371 sheet: -1.35 (0.41), residues: 135 loop : -0.41 (0.22), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 574 HIS 0.019 0.001 HIS H 204 PHE 0.011 0.001 PHE G 18 TYR 0.024 0.001 TYR A 728 ARG 0.008 0.000 ARG A 657 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 146 time to evaluate : 1.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 ASP cc_start: 0.9233 (m-30) cc_final: 0.8684 (m-30) REVERT: A 520 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8524 (mp0) REVERT: A 581 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8538 (mpt) REVERT: A 587 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8622 (pp) REVERT: A 666 MET cc_start: 0.7896 (tpp) cc_final: 0.7458 (tpp) REVERT: A 670 MET cc_start: 0.6645 (ptt) cc_final: 0.6384 (ptm) REVERT: B 403 MET cc_start: 0.2903 (mpp) cc_final: 0.2545 (mpp) REVERT: B 443 ASP cc_start: 0.3760 (m-30) cc_final: 0.3288 (t0) REVERT: B 459 MET cc_start: 0.4147 (mpp) cc_final: 0.3743 (ttp) REVERT: B 525 ILE cc_start: 0.9436 (mt) cc_final: 0.9153 (mp) REVERT: C 657 ARG cc_start: 0.8015 (ptp-110) cc_final: 0.7539 (ptt90) REVERT: C 686 MET cc_start: 0.8469 (tmm) cc_final: 0.8204 (tmm) REVERT: C 801 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9139 (tm) REVERT: D 581 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8750 (mmm) REVERT: E 160 ASN cc_start: 0.8038 (m-40) cc_final: 0.7812 (m110) REVERT: F 56 GLU cc_start: 0.8911 (pm20) cc_final: 0.8690 (pm20) REVERT: F 204 HIS cc_start: 0.6595 (OUTLIER) cc_final: 0.5795 (m-70) REVERT: F 208 ARG cc_start: 0.8257 (mpt180) cc_final: 0.8011 (ttp80) REVERT: G 74 ARG cc_start: 0.8828 (ttp80) cc_final: 0.8534 (ttm110) REVERT: G 153 ILE cc_start: 0.9392 (OUTLIER) cc_final: 0.9039 (mp) REVERT: G 202 GLU cc_start: 0.9198 (tm-30) cc_final: 0.8939 (tm-30) REVERT: G 204 HIS cc_start: 0.7483 (OUTLIER) cc_final: 0.6814 (t-90) REVERT: G 205 GLN cc_start: 0.9048 (mm-40) cc_final: 0.8491 (tm-30) outliers start: 62 outliers final: 37 residues processed: 192 average time/residue: 0.2630 time to fit residues: 78.3200 Evaluate side-chains 182 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 137 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 756 ASP Chi-restraints excluded: chain C residue 801 LEU Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain D residue 486 ASP Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 808 ILE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain G residue 191 ILE Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 71 optimal weight: 20.0000 chunk 192 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 125 optimal weight: 30.0000 chunk 52 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 177 optimal weight: 4.9990 chunk 99 optimal weight: 30.0000 chunk 17 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 HIS F 9 GLN F 160 ASN ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 HIS H 9 GLN H 132 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17308 Z= 0.338 Angle : 0.580 10.674 23504 Z= 0.302 Chirality : 0.039 0.173 2715 Planarity : 0.003 0.040 2893 Dihedral : 4.083 59.790 2427 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 4.00 % Allowed : 20.63 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.18), residues: 2195 helix: 2.67 (0.14), residues: 1369 sheet: -1.18 (0.45), residues: 128 loop : -0.40 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 574 HIS 0.023 0.001 HIS H 204 PHE 0.015 0.001 PHE A 491 TYR 0.026 0.001 TYR H 200 ARG 0.004 0.000 ARG C 481 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 139 time to evaluate : 1.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 ASP cc_start: 0.9252 (m-30) cc_final: 0.8698 (m-30) REVERT: A 520 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8556 (mp0) REVERT: A 581 MET cc_start: 0.9172 (OUTLIER) cc_final: 0.8537 (mpt) REVERT: A 587 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8628 (pp) REVERT: A 666 MET cc_start: 0.7805 (tpp) cc_final: 0.7387 (tpp) REVERT: A 670 MET cc_start: 0.6413 (ptt) cc_final: 0.6207 (ptm) REVERT: B 403 MET cc_start: 0.2956 (mpp) cc_final: 0.2475 (mpp) REVERT: B 443 ASP cc_start: 0.4127 (m-30) cc_final: 0.3779 (t0) REVERT: B 459 MET cc_start: 0.4347 (mpp) cc_final: 0.3745 (ttp) REVERT: B 492 MET cc_start: 0.1337 (mpp) cc_final: 0.1006 (mpp) REVERT: B 525 ILE cc_start: 0.9436 (mt) cc_final: 0.9157 (mp) REVERT: C 657 ARG cc_start: 0.8297 (ptp-110) cc_final: 0.7863 (ptt90) REVERT: C 686 MET cc_start: 0.8422 (tmm) cc_final: 0.8174 (tmm) REVERT: C 801 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9122 (tm) REVERT: D 403 MET cc_start: 0.4974 (mpp) cc_final: 0.4600 (mpp) REVERT: E 120 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8913 (tt) REVERT: E 160 ASN cc_start: 0.8205 (m-40) cc_final: 0.7965 (m110) REVERT: F 204 HIS cc_start: 0.6614 (OUTLIER) cc_final: 0.5633 (m-70) REVERT: F 208 ARG cc_start: 0.8187 (mpt180) cc_final: 0.7926 (ttp80) REVERT: G 74 ARG cc_start: 0.8872 (ttp80) cc_final: 0.8586 (ttm110) REVERT: G 153 ILE cc_start: 0.9394 (OUTLIER) cc_final: 0.9042 (mp) REVERT: G 202 GLU cc_start: 0.9243 (tm-30) cc_final: 0.8991 (tm-30) REVERT: G 204 HIS cc_start: 0.7456 (OUTLIER) cc_final: 0.6758 (t-90) REVERT: G 205 GLN cc_start: 0.9066 (mm-40) cc_final: 0.8526 (tm-30) outliers start: 65 outliers final: 47 residues processed: 188 average time/residue: 0.2841 time to fit residues: 81.2002 Evaluate side-chains 189 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 134 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain C residue 756 ASP Chi-restraints excluded: chain C residue 801 LEU Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain D residue 486 ASP Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 704 MET Chi-restraints excluded: chain D residue 808 ILE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 198 HIS Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 206 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 156 optimal weight: 8.9990 chunk 120 optimal weight: 20.0000 chunk 179 optimal weight: 7.9990 chunk 119 optimal weight: 9.9990 chunk 213 optimal weight: 0.5980 chunk 133 optimal weight: 0.8980 chunk 129 optimal weight: 0.6980 chunk 98 optimal weight: 9.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 9 GLN ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 204 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17308 Z= 0.241 Angle : 0.537 8.726 23504 Z= 0.277 Chirality : 0.038 0.164 2715 Planarity : 0.003 0.080 2893 Dihedral : 3.953 58.400 2427 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.52 % Allowed : 21.88 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.18), residues: 2195 helix: 2.80 (0.14), residues: 1367 sheet: -1.18 (0.45), residues: 127 loop : -0.31 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 574 HIS 0.004 0.001 HIS G 204 PHE 0.010 0.001 PHE A 491 TYR 0.015 0.001 TYR A 728 ARG 0.009 0.000 ARG A 690 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 139 time to evaluate : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 499 MET cc_start: 0.8357 (ppp) cc_final: 0.7698 (ppp) REVERT: A 515 ASP cc_start: 0.9250 (m-30) cc_final: 0.8689 (m-30) REVERT: A 520 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8506 (mp0) REVERT: A 581 MET cc_start: 0.9212 (OUTLIER) cc_final: 0.8662 (mpt) REVERT: A 587 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8612 (pp) REVERT: A 686 MET cc_start: 0.8807 (tmm) cc_final: 0.8251 (ppp) REVERT: A 717 MET cc_start: 0.9173 (ppp) cc_final: 0.8761 (ppp) REVERT: B 403 MET cc_start: 0.3024 (mpp) cc_final: 0.2554 (mpp) REVERT: B 443 ASP cc_start: 0.4177 (m-30) cc_final: 0.3763 (t0) REVERT: B 459 MET cc_start: 0.4710 (mpp) cc_final: 0.4257 (ttp) REVERT: B 525 ILE cc_start: 0.9433 (mt) cc_final: 0.9149 (mp) REVERT: C 657 ARG cc_start: 0.8312 (ptp-110) cc_final: 0.7787 (ptt90) REVERT: C 686 MET cc_start: 0.8338 (tmm) cc_final: 0.8132 (tmm) REVERT: C 801 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9123 (tm) REVERT: D 403 MET cc_start: 0.4382 (mpp) cc_final: 0.4110 (mpp) REVERT: D 581 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8690 (mmm) REVERT: E 160 ASN cc_start: 0.7963 (m-40) cc_final: 0.7739 (m110) REVERT: F 204 HIS cc_start: 0.6565 (OUTLIER) cc_final: 0.5754 (m-70) REVERT: F 208 ARG cc_start: 0.8216 (mpt180) cc_final: 0.7996 (ttp80) REVERT: G 74 ARG cc_start: 0.8844 (ttp80) cc_final: 0.8595 (ttm110) REVERT: G 153 ILE cc_start: 0.9388 (OUTLIER) cc_final: 0.9037 (mp) REVERT: G 202 GLU cc_start: 0.9215 (tm-30) cc_final: 0.8958 (tm-30) REVERT: G 204 HIS cc_start: 0.7505 (OUTLIER) cc_final: 0.6974 (t-90) REVERT: G 205 GLN cc_start: 0.9064 (mm-40) cc_final: 0.8520 (tm-30) outliers start: 57 outliers final: 42 residues processed: 183 average time/residue: 0.2764 time to fit residues: 79.0366 Evaluate side-chains 187 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 137 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain C residue 756 ASP Chi-restraints excluded: chain C residue 801 LEU Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 808 ILE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 131 optimal weight: 0.7980 chunk 85 optimal weight: 0.4980 chunk 127 optimal weight: 4.9990 chunk 64 optimal weight: 0.3980 chunk 41 optimal weight: 30.0000 chunk 135 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 chunk 105 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 167 optimal weight: 3.9990 chunk 193 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 582 GLN ** C 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 9 GLN ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17308 Z= 0.179 Angle : 0.521 9.239 23504 Z= 0.265 Chirality : 0.038 0.164 2715 Planarity : 0.003 0.071 2893 Dihedral : 3.851 56.617 2427 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.10 % Allowed : 22.42 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.18), residues: 2195 helix: 2.93 (0.14), residues: 1368 sheet: -1.24 (0.45), residues: 131 loop : -0.18 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 177 HIS 0.021 0.001 HIS H 204 PHE 0.011 0.001 PHE C 655 TYR 0.012 0.001 TYR D 728 ARG 0.009 0.000 ARG A 690 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 146 time to evaluate : 1.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 499 MET cc_start: 0.8104 (ppp) cc_final: 0.7294 (ppp) REVERT: A 515 ASP cc_start: 0.9239 (m-30) cc_final: 0.8671 (m-30) REVERT: A 520 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8420 (mp0) REVERT: A 581 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8570 (mpt) REVERT: A 587 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8629 (pp) REVERT: A 686 MET cc_start: 0.8785 (tmm) cc_final: 0.8227 (ppp) REVERT: A 717 MET cc_start: 0.9078 (ppp) cc_final: 0.8686 (ppp) REVERT: B 403 MET cc_start: 0.3005 (mpp) cc_final: 0.2612 (mpp) REVERT: B 443 ASP cc_start: 0.4199 (m-30) cc_final: 0.3675 (t0) REVERT: B 459 MET cc_start: 0.4685 (mpp) cc_final: 0.4248 (ttp) REVERT: B 492 MET cc_start: 0.1425 (mpp) cc_final: 0.1092 (mpp) REVERT: B 525 ILE cc_start: 0.9430 (mt) cc_final: 0.9137 (mp) REVERT: C 657 ARG cc_start: 0.8275 (ptp-110) cc_final: 0.7777 (ptt90) REVERT: C 801 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9102 (tm) REVERT: D 581 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8696 (mmm) REVERT: E 120 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8919 (tt) REVERT: E 160 ASN cc_start: 0.7922 (m-40) cc_final: 0.7704 (m110) REVERT: F 204 HIS cc_start: 0.6430 (OUTLIER) cc_final: 0.5847 (m-70) REVERT: F 208 ARG cc_start: 0.8228 (mpt180) cc_final: 0.7979 (ttp80) REVERT: G 74 ARG cc_start: 0.8817 (ttp80) cc_final: 0.8579 (ttm110) REVERT: G 153 ILE cc_start: 0.9370 (OUTLIER) cc_final: 0.9011 (mp) REVERT: G 202 GLU cc_start: 0.9208 (tm-30) cc_final: 0.8958 (tm-30) REVERT: G 204 HIS cc_start: 0.7474 (OUTLIER) cc_final: 0.7161 (t-90) REVERT: G 205 GLN cc_start: 0.9064 (mm-40) cc_final: 0.8518 (tm-30) outliers start: 50 outliers final: 34 residues processed: 184 average time/residue: 0.2922 time to fit residues: 83.5191 Evaluate side-chains 180 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 137 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 801 LEU Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain D residue 486 ASP Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 808 ILE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 204 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 198 optimal weight: 0.7980 chunk 119 optimal weight: 50.0000 chunk 86 optimal weight: 20.0000 chunk 155 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 179 optimal weight: 6.9990 chunk 187 optimal weight: 8.9990 chunk 197 optimal weight: 7.9990 chunk 130 optimal weight: 0.7980 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 752 GLN ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 204 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 17308 Z= 0.368 Angle : 0.607 12.108 23504 Z= 0.314 Chirality : 0.040 0.178 2715 Planarity : 0.004 0.075 2893 Dihedral : 4.031 54.661 2427 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.46 % Allowed : 22.36 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.18), residues: 2195 helix: 2.68 (0.14), residues: 1371 sheet: -0.93 (0.50), residues: 111 loop : -0.22 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 574 HIS 0.005 0.001 HIS G 204 PHE 0.025 0.001 PHE F 179 TYR 0.018 0.001 TYR B 401 ARG 0.006 0.000 ARG A 690 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 138 time to evaluate : 1.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 499 MET cc_start: 0.8346 (ppp) cc_final: 0.7425 (ppp) REVERT: A 515 ASP cc_start: 0.9230 (m-30) cc_final: 0.8670 (m-30) REVERT: A 520 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8524 (mp0) REVERT: A 581 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8568 (mpt) REVERT: A 587 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8629 (pp) REVERT: A 686 MET cc_start: 0.8823 (tmm) cc_final: 0.8253 (ppp) REVERT: A 704 MET cc_start: 0.9011 (tpp) cc_final: 0.8794 (tpp) REVERT: A 717 MET cc_start: 0.9137 (ppp) cc_final: 0.8786 (ppp) REVERT: B 403 MET cc_start: 0.3179 (mpp) cc_final: 0.2815 (mpp) REVERT: B 443 ASP cc_start: 0.4568 (m-30) cc_final: 0.4297 (t0) REVERT: B 459 MET cc_start: 0.4954 (mpp) cc_final: 0.4412 (ttp) REVERT: B 525 ILE cc_start: 0.9433 (mt) cc_final: 0.9164 (mp) REVERT: C 581 MET cc_start: 0.9037 (mtp) cc_final: 0.8835 (mtp) REVERT: C 657 ARG cc_start: 0.8378 (ptp-110) cc_final: 0.7929 (ptt90) REVERT: C 726 LYS cc_start: 0.2874 (pttt) cc_final: 0.2209 (tttt) REVERT: C 801 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9137 (tm) REVERT: E 120 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8912 (tt) REVERT: F 204 HIS cc_start: 0.6630 (OUTLIER) cc_final: 0.5713 (m-70) REVERT: F 208 ARG cc_start: 0.8355 (mpt180) cc_final: 0.8083 (ttp80) REVERT: G 74 ARG cc_start: 0.8800 (ttp80) cc_final: 0.8510 (ttm110) REVERT: G 153 ILE cc_start: 0.9397 (OUTLIER) cc_final: 0.9051 (mp) REVERT: G 202 GLU cc_start: 0.9255 (tm-30) cc_final: 0.8974 (tm-30) REVERT: G 204 HIS cc_start: 0.7432 (OUTLIER) cc_final: 0.6823 (t-90) REVERT: G 205 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8525 (tm-30) outliers start: 56 outliers final: 44 residues processed: 181 average time/residue: 0.2705 time to fit residues: 76.2002 Evaluate side-chains 188 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 136 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 756 ASP Chi-restraints excluded: chain C residue 801 LEU Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain D residue 486 ASP Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 704 MET Chi-restraints excluded: chain D residue 808 ILE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 209 optimal weight: 6.9990 chunk 128 optimal weight: 0.9980 chunk 99 optimal weight: 20.0000 chunk 145 optimal weight: 10.0000 chunk 220 optimal weight: 5.9990 chunk 202 optimal weight: 0.8980 chunk 175 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 135 optimal weight: 0.7980 chunk 107 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 overall best weight: 1.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 204 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17308 Z= 0.211 Angle : 0.556 10.565 23504 Z= 0.283 Chirality : 0.038 0.164 2715 Planarity : 0.003 0.069 2893 Dihedral : 3.974 53.931 2427 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.92 % Allowed : 22.84 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.18), residues: 2195 helix: 2.79 (0.14), residues: 1366 sheet: -0.76 (0.47), residues: 130 loop : -0.16 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 574 HIS 0.027 0.001 HIS H 204 PHE 0.023 0.001 PHE F 179 TYR 0.017 0.001 TYR B 401 ARG 0.007 0.000 ARG A 690 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 142 time to evaluate : 2.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 499 MET cc_start: 0.8217 (ppp) cc_final: 0.7198 (ppp) REVERT: A 515 ASP cc_start: 0.9232 (m-30) cc_final: 0.8661 (m-30) REVERT: A 520 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8481 (mp0) REVERT: A 581 MET cc_start: 0.9196 (OUTLIER) cc_final: 0.8690 (mpt) REVERT: A 587 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8613 (pp) REVERT: A 666 MET cc_start: 0.8792 (mtm) cc_final: 0.8256 (tmm) REVERT: A 686 MET cc_start: 0.8807 (tmm) cc_final: 0.8216 (ppp) REVERT: A 717 MET cc_start: 0.9074 (ppp) cc_final: 0.8717 (ppp) REVERT: B 403 MET cc_start: 0.3080 (mpp) cc_final: 0.2551 (mpp) REVERT: B 443 ASP cc_start: 0.4377 (m-30) cc_final: 0.4083 (t0) REVERT: B 459 MET cc_start: 0.4800 (mpp) cc_final: 0.4286 (ttp) REVERT: B 525 ILE cc_start: 0.9435 (mt) cc_final: 0.9146 (mp) REVERT: C 657 ARG cc_start: 0.8335 (ptp-110) cc_final: 0.7878 (ptt90) REVERT: C 801 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9117 (tm) REVERT: E 120 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8920 (tt) REVERT: F 204 HIS cc_start: 0.6634 (OUTLIER) cc_final: 0.5976 (m-70) REVERT: F 208 ARG cc_start: 0.8331 (mpt180) cc_final: 0.8083 (ttp80) REVERT: G 74 ARG cc_start: 0.8802 (ttp80) cc_final: 0.8578 (ttm110) REVERT: G 153 ILE cc_start: 0.9394 (OUTLIER) cc_final: 0.9048 (mp) REVERT: G 202 GLU cc_start: 0.9220 (tm-30) cc_final: 0.8954 (tm-30) REVERT: G 204 HIS cc_start: 0.7504 (OUTLIER) cc_final: 0.6996 (t-90) REVERT: G 205 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8520 (tm-30) outliers start: 47 outliers final: 35 residues processed: 176 average time/residue: 0.2699 time to fit residues: 73.8878 Evaluate side-chains 181 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 138 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 801 LEU Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 704 MET Chi-restraints excluded: chain D residue 808 ILE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 6 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 175 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 204 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.124739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.073915 restraints weight = 156482.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.075364 restraints weight = 40674.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.076367 restraints weight = 19750.248| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 17308 Z= 0.393 Angle : 0.632 12.367 23504 Z= 0.326 Chirality : 0.041 0.305 2715 Planarity : 0.004 0.074 2893 Dihedral : 4.116 52.928 2427 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.40 % Allowed : 22.84 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.18), residues: 2195 helix: 2.54 (0.14), residues: 1371 sheet: -1.07 (0.49), residues: 117 loop : -0.18 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 763 HIS 0.006 0.001 HIS H 204 PHE 0.026 0.002 PHE F 179 TYR 0.028 0.002 TYR H 200 ARG 0.006 0.000 ARG A 690 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3016.53 seconds wall clock time: 55 minutes 38.62 seconds (3338.62 seconds total)