Starting phenix.real_space_refine on Sun Mar 17 03:32:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lep_23292/03_2024/7lep_23292_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lep_23292/03_2024/7lep_23292.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lep_23292/03_2024/7lep_23292.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lep_23292/03_2024/7lep_23292.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lep_23292/03_2024/7lep_23292_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lep_23292/03_2024/7lep_23292_updated.pdb" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.020 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: 7 Type Number sf(0) Gaussians P 6 5.49 5 S 106 5.16 5 Cl 2 4.86 5 C 10959 2.51 5 N 2586 2.21 5 O 2882 1.98 5 F 18 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 443": "OD1" <-> "OD2" Residue "A PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 515": "OD1" <-> "OD2" Residue "A PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 541": "NH1" <-> "NH2" Residue "A PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 623": "OE1" <-> "OE2" Residue "A ARG 624": "NH1" <-> "NH2" Residue "A TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 793": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 427": "OD1" <-> "OD2" Residue "B ASP 490": "OD1" <-> "OD2" Residue "B PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 519": "OD1" <-> "OD2" Residue "B PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 590": "OD1" <-> "OD2" Residue "B GLU 627": "OE1" <-> "OE2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "B TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 660": "NH1" <-> "NH2" Residue "B ASP 668": "OD1" <-> "OD2" Residue "B PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 399": "OD1" <-> "OD2" Residue "C TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 427": "OE1" <-> "OE2" Residue "C TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 515": "OD1" <-> "OD2" Residue "C PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 541": "NH1" <-> "NH2" Residue "C ASP 586": "OD1" <-> "OD2" Residue "C GLU 623": "OE1" <-> "OE2" Residue "C ARG 624": "NH1" <-> "NH2" Residue "C TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 706": "OE1" <-> "OE2" Residue "C TYR 793": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 490": "OD1" <-> "OD2" Residue "D PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 590": "OD1" <-> "OD2" Residue "D ARG 628": "NH1" <-> "NH2" Residue "D TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 660": "NH1" <-> "NH2" Residue "D GLU 755": "OE1" <-> "OE2" Residue "D ASP 760": "OD1" <-> "OD2" Residue "E TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 228": "OE1" <-> "OE2" Residue "H PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 228": "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: 16559 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2844 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 403, 2843 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 12, 'TRANS': 390} Chain breaks: 1 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 87 Conformer: "B" Number of residues, atoms: 403, 2843 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 12, 'TRANS': 390} Chain breaks: 1 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 87 bond proxies already assigned to first conformer: 2903 Chain: "B" Number of atoms: 2929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2929 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 213 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 112 Chain: "C" Number of atoms: 2855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2855 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 12, 'TRANS': 390} Chain breaks: 1 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ASN:plan1': 1, 'ASP:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 84 Chain: "D" Number of atoms: 2921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2921 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 190 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 119 Chain: "E" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1092 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 3, 'TRANS': 137} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 68 Chain: "F" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1096 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 3, 'TRANS': 137} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 64 Chain: "G" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1144 Classifications: {'peptide': 164} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 1, 'TRANS': 162} Chain breaks: 3 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 81 Chain: "H" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1144 Classifications: {'peptide': 164} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 1, 'TRANS': 162} Chain breaks: 3 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 81 Chain: "A" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 94 Unusual residues: {'POV': 8, 'ZK1': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 349 Unresolved non-hydrogen angles: 421 Unresolved non-hydrogen dihedrals: 309 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'POV:plan-3': 8, 'POV:plan-2': 8, 'POV:plan-1': 8} Unresolved non-hydrogen planarities: 78 Chain: "B" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 117 Unusual residues: {'C14': 1, 'POV': 5, 'ZK1': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 184 Unresolved non-hydrogen angles: 220 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'POV:plan-3': 4, 'POV:plan-2': 4, 'POV:plan-1': 4} Unresolved non-hydrogen planarities: 37 Chain: "C" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 94 Unusual residues: {'D10': 1, 'POV': 7, 'ZK1': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 307 Unresolved non-hydrogen angles: 370 Unresolved non-hydrogen dihedrals: 272 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'POV:plan-3': 7, 'POV:plan-2': 7, 'POV:plan-1': 7} Unresolved non-hydrogen planarities: 68 Chain: "D" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 111 Unusual residues: {'POV': 6, 'ZK1': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 228 Unresolved non-hydrogen angles: 273 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-3': 5, 'POV:plan-2': 5, 'POV:plan-1': 5} Unresolved non-hydrogen planarities: 46 Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 1, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 1, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 51 Unusual residues: {'D12': 1, 'OCT': 1, 'POV': 1, 'XVD': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 1, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 51 Unusual residues: {'D12': 1, 'OCT': 1, 'POV': 1, 'XVD': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 1, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 8 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 932 SG CYS A 524 77.862 74.417 62.979 1.00 23.71 S ATOM 6721 SG CYS C 524 39.034 47.071 62.900 1.00 23.98 S Time building chain proxies: 11.33, per 1000 atoms: 0.68 Number of scatterers: 16559 At special positions: 0 Unit cell: (119.178, 122.488, 147.869, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 2 17.00 S 106 16.00 P 6 15.00 F 18 9.00 O 2882 8.00 N 2586 7.00 C 10959 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 714 " - pdb=" SG CYS A 769 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 714 " - pdb=" SG CYS C 769 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS G 90 " - pdb=" SG CYS G 100 " distance=2.04 Simple disulfide: pdb=" SG CYS H 90 " - pdb=" SG CYS H 100 " distance=2.04 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.11 Conformation dependent library (CDL) restraints added in 3.2 seconds 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4084 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 78 helices and 11 sheets defined 53.3% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.13 Creating SS restraints... Processing helix chain 'A' and resid 413 through 416 Processing helix chain 'A' and resid 420 through 432 removed outlier: 4.316A pdb=" N ALA A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS A 430 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 464 removed outlier: 3.636A pdb=" N VAL A 464 " --> pdb=" O VAL A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 484 removed outlier: 3.753A pdb=" N VAL A 484 " --> pdb=" O VAL A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 514 No H-bonds generated for 'chain 'A' and resid 512 through 514' Processing helix chain 'A' and resid 519 through 540 removed outlier: 3.962A pdb=" N VAL A 526 " --> pdb=" O TRP A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 580 Processing helix chain 'A' and resid 592 through 624 removed outlier: 4.322A pdb=" N VAL A 597 " --> pdb=" O SER A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 637 Processing helix chain 'A' and resid 650 through 657 Processing helix chain 'A' and resid 661 through 671 Processing helix chain 'A' and resid 682 through 692 Processing helix chain 'A' and resid 702 through 708 Processing helix chain 'A' and resid 740 through 752 removed outlier: 4.095A pdb=" N ALA A 745 " --> pdb=" O PRO A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 762 removed outlier: 3.694A pdb=" N LEU A 758 " --> pdb=" O ALA A 754 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 812 Processing helix chain 'B' and resid 424 through 435 Processing helix chain 'B' and resid 462 through 468 removed outlier: 3.865A pdb=" N LEU B 467 " --> pdb=" O MET B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 486 No H-bonds generated for 'chain 'B' and resid 483 through 486' Processing helix chain 'B' and resid 523 through 546 removed outlier: 3.555A pdb=" N VAL B 538 " --> pdb=" O ILE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 584 removed outlier: 3.511A pdb=" N TRP B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 625 removed outlier: 3.807A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY B 602 " --> pdb=" O GLY B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 642 Processing helix chain 'B' and resid 654 through 660 removed outlier: 4.891A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG B 660 " --> pdb=" O LYS B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 675 removed outlier: 3.759A pdb=" N MET B 674 " --> pdb=" O MET B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 695 Processing helix chain 'B' and resid 706 through 714 removed outlier: 3.628A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 755 removed outlier: 4.094A pdb=" N LEU B 748 " --> pdb=" O ASN B 744 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA B 749 " --> pdb=" O ALA B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 768 Processing helix chain 'B' and resid 789 through 818 removed outlier: 4.894A pdb=" N GLY B 794 " --> pdb=" O SER B 790 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N VAL B 795 " --> pdb=" O ASN B 791 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE B 798 " --> pdb=" O GLY B 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 416 Processing helix chain 'C' and resid 420 through 432 removed outlier: 4.375A pdb=" N ALA C 429 " --> pdb=" O ALA C 425 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS C 430 " --> pdb=" O ALA C 426 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS C 431 " --> pdb=" O GLU C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 464 removed outlier: 3.715A pdb=" N LEU C 463 " --> pdb=" O MET C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 484 removed outlier: 3.789A pdb=" N VAL C 484 " --> pdb=" O VAL C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 514 No H-bonds generated for 'chain 'C' and resid 512 through 514' Processing helix chain 'C' and resid 519 through 540 Processing helix chain 'C' and resid 569 through 580 Processing helix chain 'C' and resid 592 through 624 removed outlier: 4.184A pdb=" N VAL C 597 " --> pdb=" O SER C 593 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY C 598 " --> pdb=" O GLY C 594 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN C 615 " --> pdb=" O SER C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 637 Processing helix chain 'C' and resid 650 through 657 Processing helix chain 'C' and resid 661 through 671 Processing helix chain 'C' and resid 682 through 692 Processing helix chain 'C' and resid 702 through 711 removed outlier: 3.666A pdb=" N GLN C 710 " --> pdb=" O GLU C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 752 Processing helix chain 'C' and resid 756 through 762 Processing helix chain 'C' and resid 789 through 812 removed outlier: 3.862A pdb=" N PHE C 810 " --> pdb=" O ALA C 806 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 435 Processing helix chain 'D' and resid 465 through 468 No H-bonds generated for 'chain 'D' and resid 465 through 468' Processing helix chain 'D' and resid 483 through 486 No H-bonds generated for 'chain 'D' and resid 483 through 486' Processing helix chain 'D' and resid 523 through 546 Processing helix chain 'D' and resid 573 through 584 removed outlier: 3.757A pdb=" N PHE D 579 " --> pdb=" O ASN D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 625 removed outlier: 3.774A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 642 removed outlier: 4.100A pdb=" N LYS D 641 " --> pdb=" O GLU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 661 Processing helix chain 'D' and resid 665 through 675 removed outlier: 3.703A pdb=" N MET D 674 " --> pdb=" O MET D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 695 Processing helix chain 'D' and resid 706 through 714 removed outlier: 3.733A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 744 through 755 removed outlier: 4.185A pdb=" N LEU D 748 " --> pdb=" O ASN D 744 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA D 749 " --> pdb=" O ALA D 745 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 768 Processing helix chain 'D' and resid 789 through 818 removed outlier: 4.871A pdb=" N GLY D 794 " --> pdb=" O SER D 790 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N VAL D 795 " --> pdb=" O ASN D 791 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE D 798 " --> pdb=" O GLY D 794 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 35 removed outlier: 3.972A pdb=" N ALA E 18 " --> pdb=" O LEU E 14 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER E 19 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL E 24 " --> pdb=" O LEU E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 85 removed outlier: 4.288A pdb=" N VAL E 69 " --> pdb=" O ARG E 65 " (cutoff:3.500A) Proline residue: E 70 - end of helix removed outlier: 3.890A pdb=" N HIS E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 102 removed outlier: 3.836A pdb=" N LEU E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Proline residue: E 96 - end of helix Processing helix chain 'E' and resid 126 through 158 Processing helix chain 'F' and resid 5 through 35 removed outlier: 4.073A pdb=" N ALA F 18 " --> pdb=" O LEU F 14 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER F 19 " --> pdb=" O VAL F 15 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL F 24 " --> pdb=" O LEU F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 85 removed outlier: 4.366A pdb=" N VAL F 69 " --> pdb=" O ARG F 65 " (cutoff:3.500A) Proline residue: F 70 - end of helix removed outlier: 3.859A pdb=" N HIS F 75 " --> pdb=" O GLU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 102 removed outlier: 3.790A pdb=" N LEU F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) Proline residue: F 96 - end of helix Processing helix chain 'F' and resid 126 through 158 Processing helix chain 'G' and resid 21 through 40 removed outlier: 3.958A pdb=" N ILE G 39 " --> pdb=" O MET G 35 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER G 40 " --> pdb=" O THR G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 126 Processing helix chain 'G' and resid 129 through 149 removed outlier: 3.723A pdb=" N ARG G 149 " --> pdb=" O VAL G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 183 removed outlier: 3.766A pdb=" N VAL G 166 " --> pdb=" O GLY G 162 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY G 169 " --> pdb=" O PHE G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 231 Processing helix chain 'H' and resid 21 through 40 removed outlier: 3.957A pdb=" N ILE H 39 " --> pdb=" O MET H 35 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER H 40 " --> pdb=" O THR H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 126 Processing helix chain 'H' and resid 129 through 149 removed outlier: 3.724A pdb=" N ARG H 149 " --> pdb=" O VAL H 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 157 through 183 removed outlier: 3.766A pdb=" N VAL H 166 " --> pdb=" O GLY H 162 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY H 169 " --> pdb=" O PHE H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 231 Processing sheet with id= A, first strand: chain 'A' and resid 391 through 393 removed outlier: 3.950A pdb=" N VAL A 393 " --> pdb=" O ALA A 437 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 402 through 404 Processing sheet with id= C, first strand: chain 'A' and resid 496 through 499 Processing sheet with id= D, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.867A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 503 through 505 Processing sheet with id= F, first strand: chain 'B' and resid 646 through 648 Processing sheet with id= G, first strand: chain 'C' and resid 391 through 395 removed outlier: 4.089A pdb=" N VAL C 393 " --> pdb=" O ALA C 437 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR C 395 " --> pdb=" O ALA C 439 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 402 through 404 Processing sheet with id= I, first strand: chain 'C' and resid 496 through 499 Processing sheet with id= J, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.863A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 720 through 723 removed outlier: 3.931A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.265A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) 828 hydrogen bonds defined for protein. 2466 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: 5.10 Time building geometry restraints manager: 7.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2536 1.32 - 1.45: 5346 1.45 - 1.59: 8836 1.59 - 1.73: 4 1.73 - 1.86: 168 Bond restraints: 16890 Sorted by residual: bond pdb=" CAT ZK1 D 901 " pdb=" OAA ZK1 D 901 " ideal model delta sigma weight residual 1.214 1.401 -0.187 2.00e-02 2.50e+03 8.75e+01 bond pdb=" CAT ZK1 C 901 " pdb=" OAA ZK1 C 901 " ideal model delta sigma weight residual 1.214 1.397 -0.183 2.00e-02 2.50e+03 8.36e+01 bond pdb=" CAT ZK1 A 901 " pdb=" OAA ZK1 A 901 " ideal model delta sigma weight residual 1.214 1.397 -0.183 2.00e-02 2.50e+03 8.34e+01 bond pdb=" CAU ZK1 C 901 " pdb=" OAB ZK1 C 901 " ideal model delta sigma weight residual 1.215 1.398 -0.183 2.00e-02 2.50e+03 8.34e+01 bond pdb=" CAU ZK1 A 901 " pdb=" OAB ZK1 A 901 " ideal model delta sigma weight residual 1.215 1.397 -0.182 2.00e-02 2.50e+03 8.31e+01 ... (remaining 16885 not shown) Histogram of bond angle deviations from ideal: 97.74 - 105.03: 205 105.03 - 112.32: 8836 112.32 - 119.61: 5361 119.61 - 126.90: 8304 126.90 - 134.19: 197 Bond angle restraints: 22903 Sorted by residual: angle pdb=" N PRO F 109 " pdb=" CA PRO F 109 " pdb=" CB PRO F 109 " ideal model delta sigma weight residual 103.25 110.14 -6.89 1.05e+00 9.07e-01 4.30e+01 angle pdb=" N PRO E 109 " pdb=" CA PRO E 109 " pdb=" CB PRO E 109 " ideal model delta sigma weight residual 103.25 110.12 -6.87 1.05e+00 9.07e-01 4.28e+01 angle pdb=" O11 POV B 902 " pdb=" P POV B 902 " pdb=" O12 POV B 902 " ideal model delta sigma weight residual 97.67 109.34 -11.67 3.00e+00 1.11e-01 1.51e+01 angle pdb=" O11 POV D 902 " pdb=" P POV D 902 " pdb=" O12 POV D 902 " ideal model delta sigma weight residual 97.67 109.23 -11.56 3.00e+00 1.11e-01 1.49e+01 angle pdb=" C14 POV B 902 " pdb=" N POV B 902 " pdb=" C15 POV B 902 " ideal model delta sigma weight residual 108.02 119.56 -11.54 3.00e+00 1.11e-01 1.48e+01 ... (remaining 22898 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.47: 9418 29.47 - 58.94: 290 58.94 - 88.42: 21 88.42 - 117.89: 14 117.89 - 147.36: 8 Dihedral angle restraints: 9751 sinusoidal: 3371 harmonic: 6380 Sorted by residual: dihedral pdb=" CB CYS G 90 " pdb=" SG CYS G 90 " pdb=" SG CYS G 100 " pdb=" CB CYS G 100 " ideal model delta sinusoidal sigma weight residual 93.00 41.08 51.92 1 1.00e+01 1.00e-02 3.68e+01 dihedral pdb=" CB CYS H 90 " pdb=" SG CYS H 90 " pdb=" SG CYS H 100 " pdb=" CB CYS H 100 " ideal model delta sinusoidal sigma weight residual 93.00 41.13 51.87 1 1.00e+01 1.00e-02 3.67e+01 dihedral pdb=" CB CYS C 714 " pdb=" SG CYS C 714 " pdb=" SG CYS C 769 " pdb=" CB CYS C 769 " ideal model delta sinusoidal sigma weight residual -86.00 -131.73 45.73 1 1.00e+01 1.00e-02 2.90e+01 ... (remaining 9748 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1945 0.047 - 0.095: 572 0.095 - 0.142: 127 0.142 - 0.189: 9 0.189 - 0.237: 4 Chirality restraints: 2657 Sorted by residual: chirality pdb=" CA PRO F 109 " pdb=" N PRO F 109 " pdb=" C PRO F 109 " pdb=" CB PRO F 109 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA PRO E 109 " pdb=" N PRO E 109 " pdb=" C PRO E 109 " pdb=" CB PRO E 109 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA PHE G 130 " pdb=" N PHE G 130 " pdb=" C PHE G 130 " pdb=" CB PHE G 130 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.44e-01 ... (remaining 2654 not shown) Planarity restraints: 2760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 766 " 0.018 2.00e-02 2.50e+03 2.34e-02 1.37e+01 pdb=" CG TRP B 766 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP B 766 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 TRP B 766 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 766 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP B 766 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 766 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 766 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 766 " 0.016 2.00e-02 2.50e+03 pdb=" CH2 TRP B 766 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 417 " 0.022 2.00e-02 2.50e+03 2.10e-02 8.86e+00 pdb=" CG TYR A 417 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR A 417 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR A 417 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 417 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 417 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR A 417 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 417 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 207 " -0.024 2.00e-02 2.50e+03 2.19e-02 8.36e+00 pdb=" CG PHE G 207 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE G 207 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE G 207 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE G 207 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE G 207 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE G 207 " -0.001 2.00e-02 2.50e+03 ... (remaining 2757 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 115 2.56 - 3.14: 13975 3.14 - 3.73: 25011 3.73 - 4.31: 33464 4.31 - 4.90: 56802 Nonbonded interactions: 129367 Sorted by model distance: nonbonded pdb=" NH1 ARG D 485 " pdb=" OAA ZK1 D 901 " model vdw 1.973 2.496 nonbonded pdb=" O SER C 543 " pdb=" OH TYR H 226 " model vdw 2.170 2.440 nonbonded pdb=" O ILE A 498 " pdb=" ND2 ASN A 705 " model vdw 2.190 2.520 nonbonded pdb=" O ILE C 498 " pdb=" ND2 ASN C 705 " model vdw 2.206 2.520 nonbonded pdb=" OG1 THR A 478 " pdb=" OE2 GLU D 755 " model vdw 2.216 2.440 ... (remaining 129362 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 394 or (resid 395 and (name N or name CA or na \ me C or name O or name CB )) or resid 396 or resid 398 or resid 400 through 403 \ or (resid 405 through 407 and (name N or name CA or name C or name O or name CB \ )) or resid 412 through 414 or resid 417 through 422 or resid 424 through 429 or \ (resid 430 and (name N or name CA or name C or name O or name CB )) or resid 43 \ 1 or resid 436 or resid 440 through 441 or resid 443 through 451 or resid 453 th \ rough 454 or resid 456 through 461 or (resid 462 and (name N or name CA or name \ C or name O or name CB )) or resid 463 through 466 or resid 468 or resid 471 or \ resid 473 through 481 or (resid 482 through 483 and (name N or name CA or name C \ or name O or name CB )) or resid 484 through 506 or (resid 507 and (name N or n \ ame CA or name C or name O or name CB )) or resid 508 through 509 or (resid 510 \ and (name N or name CA or name C or name O or name CB or name CG1)) or resid 511 \ through 543 or (resid 565 and (name N or name CA or name C or name O or name CB \ )) or resid 566 through 581 or resid 583 through 629 or (resid 630 and (name N \ or name CA or name C or name O or name CB )) or resid 631 through 635 or (resid \ 637 through 640 and (name N or name CA or name C or name O or name CB )) or resi \ d 641 through 646 or resid 649 or resid 651 through 661 or (resid 662 and (name \ N or name CA or name C or name O or name CB )) or resid 665 through 667 or resid \ 669 or (resid 670 and (name N or name CA or name C or name O or name CB )) or r \ esid 672 through 675 or (resid 676 and (name N or name CA or name C or name O or \ name CB )) or resid 677 through 678 or resid 681 through 683 or resid 685 or re \ sid 687 through 689 or (resid 690 through 691 and (name N or name CA or name C o \ r name O or name CB )) or resid 693 through 695 or resid 697 or resid 699 throug \ h 729 or resid 731 through 736 or resid 738 or resid 742 through 749 or resid 75 \ 1 or resid 753 or resid 755 through 759 or resid 761 through 770 or (resid 776 t \ hrough 777 and (name N or name CA or name C or name O or name CB )) or resid 779 \ through 795 or resid 797 through 803 or resid 805 through 811 or (resid 812 thr \ ough 813 and (name N or name CA or name C or name O or name CB )) or resid 907 o \ r resid 909)) selection = (chain 'B' and (resid 397 through 400 or (resid 402 and (name N or name CA or na \ me C or name O or name CB )) or resid 404 through 407 or resid 409 through 411 o \ r resid 416 through 418 or resid 421 through 426 or resid 428 through 435 or res \ id 440 or resid 444 through 445 or resid 447 through 452 or (resid 453 through 4 \ 55 and (name N or name CA or name C or name O or name CB )) or (resid 457 throug \ h 458 and (name N or name CA or name C or name O or name CB )) or resid 460 thro \ ugh 470 or resid 472 or resid 475 or resid 477 through 486 or (resid 487 and (na \ me N or name CA or name C or name O or name CB )) or resid 488 through 489 or (r \ esid 490 and (name N or name CA or name C or name O or name CB )) or resid 491 t \ hrough 507 or (resid 508 through 509 and (name N or name CA or name C or name O \ or name CB )) or resid 510 through 513 or (resid 514 and (name N or name CA or n \ ame C or name O or name CB or name CG1)) or resid 515 through 585 or resid 587 t \ hrough 639 or resid 641 through 650 or resid 653 or resid 655 through 659 or (re \ sid 660 through 661 and (name N or name CA or name C or name O or name CB )) or \ resid 662 through 665 or (resid 666 and (name N or name CA or name C or name O o \ r name CB )) or (resid 669 and (name N or name CA or name C or name O or name CB \ )) or resid 670 through 671 or resid 673 through 674 or resid 676 through 682 o \ r (resid 685 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 86 through 687 or resid 689 or (resid 691 through 692 and (name N or name CA or \ name C or name O or name CB )) or resid 693 through 695 or resid 697 through 699 \ or resid 701 or resid 703 through 714 or (resid 715 through 716 and (name N or \ name CA or name C or name O or name CB )) or resid 717 through 733 or resid 735 \ through 740 or resid 742 or resid 746 through 753 or resid 755 or resid 757 or r \ esid 759 through 763 or resid 765 through 768 or (resid 769 and (name N or name \ CA or name C or name O or name CB )) or resid 770 through 774 or resid 780 throu \ gh 781 or (resid 783 through 784 and (name N or name CA or name C or name O or n \ ame CB )) or resid 785 through 799 or resid 801 through 807 or resid 809 through \ 815 or (resid 816 through 817 and (name N or name CA or name C or name O or nam \ e CB )) or resid 905 or (resid 907 and (name C21 or name C22 or name C23 or name \ C24 or name C25)))) selection = (chain 'C' and (resid 393 through 394 or (resid 395 and (name N or name CA or na \ me C or name O or name CB )) or resid 396 or resid 398 or resid 400 through 403 \ or (resid 405 through 407 and (name N or name CA or name C or name O or name CB \ )) or resid 412 through 414 or resid 417 through 422 or resid 424 through 429 or \ (resid 430 and (name N or name CA or name C or name O or name CB )) or resid 43 \ 1 or resid 436 or resid 440 through 441 or resid 443 through 451 or resid 453 th \ rough 454 or resid 456 through 461 or (resid 462 and (name N or name CA or name \ C or name O or name CB )) or resid 463 through 466 or resid 468 or resid 471 or \ resid 473 through 481 or (resid 482 through 483 and (name N or name CA or name C \ or name O or name CB )) or resid 484 through 506 or (resid 507 and (name N or n \ ame CA or name C or name O or name CB )) or resid 508 through 509 or (resid 510 \ and (name N or name CA or name C or name O or name CB or name CG1)) or resid 511 \ through 543 or (resid 565 and (name N or name CA or name C or name O or name CB \ )) or resid 566 through 581 or resid 583 through 629 or (resid 630 and (name N \ or name CA or name C or name O or name CB )) or resid 631 through 635 or (resid \ 637 through 640 and (name N or name CA or name C or name O or name CB )) or resi \ d 641 through 646 or resid 649 or resid 651 through 662 or resid 665 through 667 \ or resid 669 or (resid 670 and (name N or name CA or name C or name O or name C \ B )) or resid 672 through 675 or (resid 676 and (name N or name CA or name C or \ name O or name CB )) or resid 677 through 678 or resid 681 through 683 or resid \ 685 or resid 687 through 689 or (resid 690 through 691 and (name N or name CA or \ name C or name O or name CB )) or resid 693 through 695 or resid 697 or resid 6 \ 99 through 729 or resid 731 through 736 or resid 738 or resid 742 through 749 or \ resid 751 or resid 753 or resid 755 through 759 or resid 761 through 770 or (re \ sid 776 through 777 and (name N or name CA or name C or name O or name CB )) or \ resid 779 through 795 or resid 797 through 803 or resid 805 through 811 or (resi \ d 812 through 813 and (name N or name CA or name C or name O or name CB )) or re \ sid 907 or (resid 909 and (name C21 or name C22 or name C23 or name C24 or name \ C25)))) selection = (chain 'D' and (resid 397 through 400 or (resid 402 and (name N or name CA or na \ me C or name O or name CB )) or resid 404 through 407 or resid 409 through 411 o \ r resid 416 through 418 or resid 421 through 426 or resid 428 through 435 or res \ id 440 or resid 444 through 445 or resid 447 through 452 or (resid 453 through 4 \ 55 and (name N or name CA or name C or name O or name CB )) or (resid 457 throug \ h 458 and (name N or name CA or name C or name O or name CB )) or resid 460 thro \ ugh 470 or resid 472 or resid 475 or resid 477 through 486 or (resid 487 and (na \ me N or name CA or name C or name O or name CB )) or resid 488 through 489 or (r \ esid 490 and (name N or name CA or name C or name O or name CB )) or resid 491 t \ hrough 507 or (resid 508 through 509 and (name N or name CA or name C or name O \ or name CB )) or resid 510 or (resid 511 and (name N or name CA or name C or nam \ e O or name CB )) or resid 512 through 585 or resid 587 through 639 or resid 641 \ through 650 or resid 653 or resid 655 through 659 or (resid 660 through 661 and \ (name N or name CA or name C or name O or name CB )) or resid 662 through 665 o \ r (resid 666 and (name N or name CA or name C or name O or name CB )) or (resid \ 669 and (name N or name CA or name C or name O or name CB )) or resid 670 throug \ h 671 or resid 673 through 674 or resid 676 through 682 or (resid 685 and (name \ N or name CA or name C or name O or name CB )) or resid 686 through 687 or resid \ 689 or (resid 691 through 692 and (name N or name CA or name C or name O or nam \ e CB )) or resid 693 through 695 or resid 697 through 699 or resid 701 or resid \ 703 through 714 or (resid 715 through 716 and (name N or name CA or name C or na \ me O or name CB )) or resid 717 through 733 or resid 735 through 740 or resid 74 \ 2 or resid 746 through 753 or resid 755 or resid 757 or resid 759 through 763 or \ resid 765 through 768 or (resid 769 and (name N or name CA or name C or name O \ or name CB )) or resid 770 through 774 or resid 780 through 781 or (resid 783 th \ rough 784 and (name N or name CA or name C or name O or name CB )) or resid 785 \ through 799 or resid 801 through 807 or resid 809 through 817 or (resid 905 and \ (name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C2 \ 7 or name C28)) or (resid 907 and (name C21 or name C22 or name C23 or name C24 \ or name C25)))) } ncs_group { reference = chain 'E' selection = (chain 'F' and (resid 2 through 57 or (resid 58 through 59 and (name N or name C \ A or name C or name O or name CB )) or resid 60 through 160 or resid 201)) } ncs_group { reference = chain 'G' selection = chain 'H' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.030 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: 14.440 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 49.250 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.130 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 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 : 0.010 0.187 16890 Z= 0.658 Angle : 0.859 11.671 22903 Z= 0.421 Chirality : 0.046 0.237 2657 Planarity : 0.004 0.046 2760 Dihedral : 15.516 147.361 5649 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.28 % Favored : 94.58 % Rotamer: Outliers : 0.40 % Allowed : 0.67 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.48 (0.18), residues: 2178 helix: 0.84 (0.15), residues: 1267 sheet: -1.64 (0.53), residues: 115 loop : -2.03 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP B 766 HIS 0.005 0.002 HIS E 75 PHE 0.049 0.003 PHE G 207 TYR 0.051 0.002 TYR A 417 ARG 0.011 0.001 ARG A 624 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 228 time to evaluate : 1.811 Fit side-chains revert: symmetry clash REVERT: B 766 TRP cc_start: 0.6971 (m-10) cc_final: 0.6507 (m-10) REVERT: B 769 ASP cc_start: 0.8275 (m-30) cc_final: 0.7957 (m-30) REVERT: D 482 THR cc_start: 0.8483 (t) cc_final: 0.8232 (m) REVERT: D 769 ASP cc_start: 0.8351 (m-30) cc_final: 0.8049 (m-30) REVERT: E 132 GLN cc_start: 0.6977 (tp40) cc_final: 0.6722 (tp40) REVERT: H 103 ILE cc_start: 0.8519 (mm) cc_final: 0.8255 (mm) outliers start: 4 outliers final: 0 residues processed: 229 average time/residue: 0.2612 time to fit residues: 91.6968 Evaluate side-chains 183 residues out of total 1778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 8.9990 chunk 166 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 112 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 172 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 199 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 744 ASN ** C 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 418 ASN D 435 HIS G 172 ASN H 172 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16890 Z= 0.191 Angle : 0.524 7.837 22903 Z= 0.268 Chirality : 0.038 0.157 2657 Planarity : 0.003 0.038 2760 Dihedral : 10.665 128.302 2703 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.01 % Allowed : 7.71 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.27 (0.18), residues: 2178 helix: 1.55 (0.15), residues: 1265 sheet: -1.67 (0.56), residues: 106 loop : -1.86 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 766 HIS 0.002 0.001 HIS F 101 PHE 0.018 0.002 PHE D 574 TYR 0.022 0.001 TYR C 446 ARG 0.004 0.000 ARG B 819 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 202 time to evaluate : 1.922 Fit side-chains revert: symmetry clash REVERT: B 715 ARG cc_start: 0.7172 (mmp80) cc_final: 0.6911 (mmt-90) REVERT: C 704 MET cc_start: 0.7860 (tpt) cc_final: 0.7642 (tpt) REVERT: D 482 THR cc_start: 0.8366 (t) cc_final: 0.8138 (m) REVERT: D 769 ASP cc_start: 0.8353 (m-30) cc_final: 0.8081 (m-30) outliers start: 13 outliers final: 10 residues processed: 214 average time/residue: 0.2661 time to fit residues: 88.5900 Evaluate side-chains 189 residues out of total 1778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 179 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain C residue 624 ARG Chi-restraints excluded: chain C residue 808 ILE Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 425 CYS Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain H residue 176 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 111 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 166 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 216 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 198 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 744 ASN C 565 ASN ** C 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS G 183 ASN H 183 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 16890 Z= 0.381 Angle : 0.586 7.248 22903 Z= 0.300 Chirality : 0.041 0.179 2657 Planarity : 0.004 0.074 2760 Dihedral : 9.897 109.712 2703 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.14 % Allowed : 11.53 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.20 (0.18), residues: 2178 helix: 1.51 (0.15), residues: 1251 sheet: -1.60 (0.56), residues: 106 loop : -1.88 (0.19), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 766 HIS 0.004 0.001 HIS E 75 PHE 0.027 0.002 PHE A 491 TYR 0.030 0.002 TYR C 446 ARG 0.004 0.001 ARG C 624 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 191 time to evaluate : 1.839 Fit side-chains revert: symmetry clash REVERT: A 404 LEU cc_start: 0.7409 (mm) cc_final: 0.7167 (mt) REVERT: A 445 LYS cc_start: 0.7754 (ttpt) cc_final: 0.7494 (ttpt) REVERT: B 766 TRP cc_start: 0.7040 (m100) cc_final: 0.6578 (m-10) REVERT: D 769 ASP cc_start: 0.8330 (m-30) cc_final: 0.8058 (m-30) outliers start: 30 outliers final: 24 residues processed: 216 average time/residue: 0.2658 time to fit residues: 87.8662 Evaluate side-chains 202 residues out of total 1778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 178 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 722 ASN Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 816 TYR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 565 ASN Chi-restraints excluded: chain C residue 624 ARG Chi-restraints excluded: chain C residue 808 ILE Chi-restraints excluded: chain D residue 425 CYS Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 785 SER Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 58 GLU Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 183 ASN Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 183 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 3.9990 chunk 150 optimal weight: 0.0970 chunk 103 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 134 optimal weight: 0.5980 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 190 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 744 ASN C 565 ASN D 435 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16890 Z= 0.201 Angle : 0.489 7.489 22903 Z= 0.254 Chirality : 0.038 0.143 2657 Planarity : 0.003 0.065 2760 Dihedral : 9.209 95.643 2703 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.88 % Allowed : 13.87 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.51 (0.19), residues: 2178 helix: 1.79 (0.15), residues: 1255 sheet: -1.63 (0.51), residues: 122 loop : -1.79 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 762 HIS 0.002 0.001 HIS E 75 PHE 0.019 0.002 PHE E 31 TYR 0.023 0.001 TYR C 446 ARG 0.004 0.000 ARG D 660 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 196 time to evaluate : 1.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 404 LEU cc_start: 0.7299 (mm) cc_final: 0.7072 (mt) REVERT: A 445 LYS cc_start: 0.7798 (ttpt) cc_final: 0.7480 (ttpt) REVERT: A 670 MET cc_start: 0.6238 (mtp) cc_final: 0.6033 (mtm) REVERT: B 766 TRP cc_start: 0.7104 (m100) cc_final: 0.6570 (m-10) REVERT: D 766 TRP cc_start: 0.8488 (m100) cc_final: 0.8117 (m100) REVERT: D 769 ASP cc_start: 0.8331 (m-30) cc_final: 0.8055 (m-30) outliers start: 26 outliers final: 20 residues processed: 218 average time/residue: 0.2691 time to fit residues: 90.0408 Evaluate side-chains 200 residues out of total 1778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 180 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 722 ASN Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 744 ASN Chi-restraints excluded: chain C residue 565 ASN Chi-restraints excluded: chain C residue 624 ARG Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 808 ILE Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain F residue 58 GLU Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain H residue 176 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 7.9990 chunk 120 optimal weight: 0.1980 chunk 3 optimal weight: 0.9990 chunk 158 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 181 optimal weight: 0.9990 chunk 146 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 190 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 GLN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 744 ASN C 565 ASN G 183 ASN H 183 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16890 Z= 0.284 Angle : 0.517 7.543 22903 Z= 0.267 Chirality : 0.039 0.159 2657 Planarity : 0.003 0.061 2760 Dihedral : 9.035 96.213 2703 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.55 % Allowed : 14.88 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.51 (0.19), residues: 2178 helix: 1.79 (0.15), residues: 1255 sheet: -1.50 (0.56), residues: 106 loop : -1.80 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 203 HIS 0.003 0.001 HIS E 75 PHE 0.026 0.002 PHE F 31 TYR 0.022 0.002 TYR C 446 ARG 0.004 0.000 ARG B 660 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 189 time to evaluate : 1.886 Fit side-chains REVERT: B 766 TRP cc_start: 0.7201 (m100) cc_final: 0.6755 (m-10) REVERT: D 503 MET cc_start: 0.8008 (ttt) cc_final: 0.7796 (ttt) REVERT: D 766 TRP cc_start: 0.8513 (m100) cc_final: 0.8129 (m100) REVERT: D 769 ASP cc_start: 0.8257 (m-30) cc_final: 0.8006 (m-30) outliers start: 36 outliers final: 29 residues processed: 219 average time/residue: 0.2600 time to fit residues: 88.0844 Evaluate side-chains 210 residues out of total 1778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 181 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 722 ASN Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 565 ASN Chi-restraints excluded: chain C residue 624 ARG Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 808 ILE Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 425 CYS Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 785 SER Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 183 ASN Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 183 ASN Chi-restraints excluded: chain H residue 220 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 3.9990 chunk 191 optimal weight: 0.0470 chunk 42 optimal weight: 9.9990 chunk 124 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 212 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 744 ASN G 183 ASN H 183 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16890 Z= 0.203 Angle : 0.490 8.517 22903 Z= 0.252 Chirality : 0.038 0.152 2657 Planarity : 0.003 0.052 2760 Dihedral : 8.548 95.309 2703 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.68 % Allowed : 15.55 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.71 (0.19), residues: 2178 helix: 1.95 (0.15), residues: 1263 sheet: -1.48 (0.55), residues: 106 loop : -1.76 (0.20), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 762 HIS 0.002 0.001 HIS F 75 PHE 0.019 0.001 PHE F 31 TYR 0.022 0.001 TYR C 446 ARG 0.005 0.000 ARG D 660 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 189 time to evaluate : 1.784 Fit side-chains REVERT: B 766 TRP cc_start: 0.7256 (m100) cc_final: 0.6866 (m-10) REVERT: D 766 TRP cc_start: 0.8467 (m100) cc_final: 0.8021 (m100) REVERT: D 769 ASP cc_start: 0.8260 (m-30) cc_final: 0.8000 (m-30) outliers start: 38 outliers final: 29 residues processed: 221 average time/residue: 0.2620 time to fit residues: 88.8843 Evaluate side-chains 202 residues out of total 1778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 173 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 722 ASN Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 624 ARG Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 808 ILE Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 784 THR Chi-restraints excluded: chain D residue 785 SER Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 183 ASN Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 183 ASN Chi-restraints excluded: chain H residue 220 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 121 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 chunk 179 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 212 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 744 ASN ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 565 ASN G 183 ASN H 183 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16890 Z= 0.219 Angle : 0.495 9.600 22903 Z= 0.253 Chirality : 0.038 0.148 2657 Planarity : 0.003 0.048 2760 Dihedral : 8.376 95.392 2703 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.68 % Allowed : 16.29 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.78 (0.19), residues: 2178 helix: 2.02 (0.15), residues: 1261 sheet: -1.47 (0.54), residues: 106 loop : -1.71 (0.20), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 762 HIS 0.002 0.001 HIS F 75 PHE 0.017 0.001 PHE A 491 TYR 0.023 0.001 TYR C 446 ARG 0.008 0.001 ARG D 660 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 178 time to evaluate : 1.941 Fit side-chains revert: symmetry clash REVERT: B 463 MET cc_start: 0.7201 (mtt) cc_final: 0.6974 (mtt) REVERT: B 508 GLN cc_start: 0.7573 (pm20) cc_final: 0.7316 (pm20) REVERT: B 766 TRP cc_start: 0.7332 (m100) cc_final: 0.6940 (m-10) REVERT: D 629 MET cc_start: 0.7515 (mmt) cc_final: 0.7143 (mmt) REVERT: D 766 TRP cc_start: 0.8465 (m100) cc_final: 0.8054 (m100) REVERT: D 769 ASP cc_start: 0.8270 (m-30) cc_final: 0.8004 (m-30) REVERT: F 136 TRP cc_start: 0.6822 (m100) cc_final: 0.6574 (m100) outliers start: 38 outliers final: 35 residues processed: 211 average time/residue: 0.2633 time to fit residues: 86.2446 Evaluate side-chains 213 residues out of total 1778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 178 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 722 ASN Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 565 ASN Chi-restraints excluded: chain C residue 624 ARG Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 808 ILE Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 784 THR Chi-restraints excluded: chain D residue 785 SER Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 183 ASN Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 183 ASN Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain H residue 220 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 134 optimal weight: 0.6980 chunk 144 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 166 optimal weight: 0.6980 chunk 192 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 744 ASN ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 183 ASN H 183 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16890 Z= 0.259 Angle : 0.511 10.154 22903 Z= 0.261 Chirality : 0.038 0.147 2657 Planarity : 0.003 0.046 2760 Dihedral : 8.375 95.538 2703 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.82 % Allowed : 16.62 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.75 (0.19), residues: 2178 helix: 1.97 (0.15), residues: 1263 sheet: -1.46 (0.54), residues: 106 loop : -1.69 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 203 HIS 0.003 0.001 HIS E 75 PHE 0.018 0.002 PHE A 491 TYR 0.022 0.001 TYR C 446 ARG 0.006 0.001 ARG D 660 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 183 time to evaluate : 1.855 Fit side-chains REVERT: B 463 MET cc_start: 0.7192 (mtt) cc_final: 0.6959 (mtt) REVERT: B 508 GLN cc_start: 0.7566 (pm20) cc_final: 0.7305 (pm20) REVERT: B 766 TRP cc_start: 0.7485 (m100) cc_final: 0.6880 (m-10) REVERT: C 670 MET cc_start: 0.6433 (mtp) cc_final: 0.6165 (mtm) REVERT: D 629 MET cc_start: 0.7553 (mmt) cc_final: 0.7301 (mmt) REVERT: D 766 TRP cc_start: 0.8474 (m100) cc_final: 0.8058 (m100) REVERT: D 769 ASP cc_start: 0.8260 (m-30) cc_final: 0.7988 (m-30) REVERT: F 91 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7030 (tt) REVERT: F 136 TRP cc_start: 0.6813 (m100) cc_final: 0.6578 (m100) outliers start: 40 outliers final: 35 residues processed: 218 average time/residue: 0.2583 time to fit residues: 87.3081 Evaluate side-chains 214 residues out of total 1778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 178 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 722 ASN Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 624 ARG Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 808 ILE Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 425 CYS Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 784 THR Chi-restraints excluded: chain D residue 785 SER Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain H residue 220 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 0.9990 chunk 185 optimal weight: 10.0000 chunk 197 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 86 optimal weight: 0.2980 chunk 155 optimal weight: 0.0000 chunk 60 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 186 optimal weight: 0.7980 chunk 196 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 744 ASN ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 565 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16890 Z= 0.171 Angle : 0.473 10.058 22903 Z= 0.241 Chirality : 0.037 0.138 2657 Planarity : 0.003 0.045 2760 Dihedral : 7.703 94.158 2703 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.35 % Allowed : 17.36 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.99 (0.19), residues: 2178 helix: 2.23 (0.15), residues: 1258 sheet: -1.45 (0.54), residues: 106 loop : -1.67 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 762 HIS 0.002 0.000 HIS F 75 PHE 0.014 0.001 PHE C 491 TYR 0.022 0.001 TYR C 446 ARG 0.006 0.000 ARG D 660 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 195 time to evaluate : 1.718 Fit side-chains REVERT: B 762 LEU cc_start: 0.8898 (tp) cc_final: 0.8697 (tp) REVERT: B 766 TRP cc_start: 0.7349 (m100) cc_final: 0.6604 (m-10) REVERT: D 766 TRP cc_start: 0.8379 (m100) cc_final: 0.7780 (m100) REVERT: D 769 ASP cc_start: 0.8291 (m-30) cc_final: 0.8013 (m-30) REVERT: F 91 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.6946 (tt) REVERT: F 136 TRP cc_start: 0.6810 (m100) cc_final: 0.6581 (m100) outliers start: 33 outliers final: 28 residues processed: 222 average time/residue: 0.2655 time to fit residues: 91.0003 Evaluate side-chains 209 residues out of total 1778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 180 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 565 ASN Chi-restraints excluded: chain C residue 624 ARG Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 808 ILE Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 784 THR Chi-restraints excluded: chain D residue 785 SER Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 176 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 0.0770 chunk 127 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 219 optimal weight: 0.0070 chunk 201 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 134 optimal weight: 0.7980 chunk 107 optimal weight: 9.9990 chunk 138 optimal weight: 0.9990 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 744 ASN ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16890 Z= 0.173 Angle : 0.486 10.819 22903 Z= 0.247 Chirality : 0.037 0.142 2657 Planarity : 0.003 0.043 2760 Dihedral : 7.507 94.859 2703 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.48 % Allowed : 17.02 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.07 (0.19), residues: 2178 helix: 2.30 (0.15), residues: 1257 sheet: -1.45 (0.53), residues: 106 loop : -1.65 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 762 HIS 0.002 0.000 HIS F 75 PHE 0.013 0.001 PHE C 491 TYR 0.021 0.001 TYR C 446 ARG 0.006 0.000 ARG D 660 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 190 time to evaluate : 1.817 Fit side-chains REVERT: B 508 GLN cc_start: 0.7581 (pm20) cc_final: 0.7289 (pm20) REVERT: B 766 TRP cc_start: 0.7306 (m100) cc_final: 0.6622 (m-10) REVERT: C 670 MET cc_start: 0.6396 (mtp) cc_final: 0.6114 (mtm) REVERT: D 769 ASP cc_start: 0.8289 (m-30) cc_final: 0.8016 (m-30) REVERT: F 91 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.6936 (tt) REVERT: F 136 TRP cc_start: 0.6812 (m100) cc_final: 0.6594 (m100) outliers start: 35 outliers final: 30 residues processed: 220 average time/residue: 0.2557 time to fit residues: 87.2365 Evaluate side-chains 209 residues out of total 1778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 178 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 624 ARG Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 808 ILE Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 785 SER Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 220 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 48 optimal weight: 0.3980 chunk 174 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 179 optimal weight: 0.0020 chunk 22 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 153 optimal weight: 0.6980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 744 ASN ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 565 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.182928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.144706 restraints weight = 20661.255| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 2.28 r_work: 0.3795 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3666 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3628 r_free = 0.3628 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3628 r_free = 0.3628 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16890 Z= 0.172 Angle : 0.490 10.839 22903 Z= 0.249 Chirality : 0.037 0.149 2657 Planarity : 0.003 0.042 2760 Dihedral : 7.285 94.732 2703 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.48 % Allowed : 17.49 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.08 (0.19), residues: 2178 helix: 2.26 (0.15), residues: 1270 sheet: -1.55 (0.44), residues: 142 loop : -1.59 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 762 HIS 0.002 0.000 HIS F 75 PHE 0.021 0.001 PHE D 658 TYR 0.020 0.001 TYR D 405 ARG 0.006 0.000 ARG D 660 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3493.06 seconds wall clock time: 63 minutes 31.62 seconds (3811.62 seconds total)