Starting phenix.real_space_refine on Sun Jan 19 19:42:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h2t_34443/01_2025/8h2t_34443.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h2t_34443/01_2025/8h2t_34443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h2t_34443/01_2025/8h2t_34443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h2t_34443/01_2025/8h2t_34443.map" model { file = "/net/cci-nas-00/data/ceres_data/8h2t_34443/01_2025/8h2t_34443.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h2t_34443/01_2025/8h2t_34443.cif" } resolution = 2.59 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= 1.000 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: 5 Type Number sf(0) Gaussians Fe 9 7.16 5 S 87 5.16 5 C 9066 2.51 5 N 2568 2.21 5 O 2640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 14370 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 3467 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 435, 3456 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 412} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 435, 3456 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 412} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3537 Chain: "A" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1305 Classifications: {'peptide': 157} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 149} Chain: "D" Number of atoms: 3467 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 435, 3456 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 412} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 435, 3456 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 412} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3537 Chain: "E" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1305 Classifications: {'peptide': 157} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 149} Chain: "G" Number of atoms: 3467 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 435, 3456 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 412} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 435, 3456 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 412} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3537 Chain: "H" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1305 Classifications: {'peptide': 157} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 149} Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 18 Unusual residues: {' FE': 1, 'FES': 1, 'IAC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 18 Unusual residues: {' FE': 1, 'FES': 1, 'IAC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 18 Unusual residues: {' FE': 1, 'FES': 1, 'IAC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 681 SG CYS B 85 63.869 23.859 63.621 1.00 77.23 S ATOM 837 SG CYS B 106 64.771 24.572 60.097 1.00 86.23 S ATOM 5453 SG CYS D 85 92.651 68.268 63.635 1.00 82.70 S ATOM 5609 SG CYS D 106 91.640 68.795 60.069 1.00 84.01 S ATOM 10225 SG CYS G 85 39.814 71.048 63.604 1.00 79.87 S ATOM 10381 SG CYS G 106 39.938 69.893 60.076 1.00 85.39 S Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AARG B 230 " occ=0.49 ... (20 atoms not shown) pdb=" NH2BARG B 230 " occ=0.51 residue: pdb=" N AARG D 230 " occ=0.49 ... (20 atoms not shown) pdb=" NH2BARG D 230 " occ=0.51 residue: pdb=" N AARG G 230 " occ=0.46 ... (20 atoms not shown) pdb=" NH2BARG G 230 " occ=0.54 Time building chain proxies: 13.60, per 1000 atoms: 0.95 Number of scatterers: 14370 At special positions: 0 Unit cell: (121.55, 120.7, 95.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 9 26.01 S 87 16.00 O 2640 8.00 N 2568 7.00 C 9066 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.74 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES B 501 " pdb="FE1 FES B 501 " - pdb=" ND1 HIS B 87 " pdb="FE1 FES B 501 " - pdb=" ND1 HIS B 109 " pdb="FE2 FES B 501 " - pdb=" SG CYS B 106 " pdb="FE2 FES B 501 " - pdb=" SG CYS B 85 " pdb=" FES D 501 " pdb="FE1 FES D 501 " - pdb=" ND1 HIS D 109 " pdb="FE1 FES D 501 " - pdb=" ND1 HIS D 87 " pdb="FE2 FES D 501 " - pdb=" SG CYS D 106 " pdb="FE2 FES D 501 " - pdb=" SG CYS D 85 " pdb=" FES G 501 " pdb="FE1 FES G 501 " - pdb=" ND1 HIS G 87 " pdb="FE1 FES G 501 " - pdb=" ND1 HIS G 109 " pdb="FE2 FES G 501 " - pdb=" SG CYS G 106 " pdb="FE2 FES G 501 " - pdb=" SG CYS G 85 " Number of angles added : 9 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3324 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 24 sheets defined 37.8% alpha, 33.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'B' and resid 7 through 13 Processing helix chain 'B' and resid 22 through 27 removed outlier: 3.553A pdb=" N THR B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 37 Processing helix chain 'B' and resid 50 through 52 No H-bonds generated for 'chain 'B' and resid 50 through 52' Processing helix chain 'B' and resid 124 through 128 Processing helix chain 'B' and resid 165 through 171 Processing helix chain 'B' and resid 174 through 183 Processing helix chain 'B' and resid 203 through 210 removed outlier: 3.976A pdb=" N PHE B 207 " --> pdb=" O ASN B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 213 No H-bonds generated for 'chain 'B' and resid 211 through 213' Processing helix chain 'B' and resid 216 through 221 Processing helix chain 'B' and resid 221 through 233 removed outlier: 4.073A pdb=" N THR B 227 " --> pdb=" O SER B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 249 Processing helix chain 'B' and resid 250 through 253 Processing helix chain 'B' and resid 254 through 262 removed outlier: 3.687A pdb=" N PHE B 258 " --> pdb=" O ASP B 254 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY B 262 " --> pdb=" O PHE B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 297 Processing helix chain 'B' and resid 298 through 307 Processing helix chain 'B' and resid 352 through 368 removed outlier: 4.464A pdb=" N LEU B 356 " --> pdb=" O PRO B 352 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER B 368 " --> pdb=" O ARG B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 388 Processing helix chain 'B' and resid 403 through 409 removed outlier: 3.595A pdb=" N LYS B 408 " --> pdb=" O SER B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 435 removed outlier: 3.709A pdb=" N ARG B 423 " --> pdb=" O GLU B 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 24 Processing helix chain 'A' and resid 26 through 32 removed outlier: 3.589A pdb=" N ALA A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 73 removed outlier: 3.626A pdb=" N LEU A 72 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 81 removed outlier: 3.632A pdb=" N GLN A 81 " --> pdb=" O PHE A 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 13 Processing helix chain 'D' and resid 22 through 27 removed outlier: 3.553A pdb=" N THR D 26 " --> pdb=" O ARG D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 37 Processing helix chain 'D' and resid 50 through 52 No H-bonds generated for 'chain 'D' and resid 50 through 52' Processing helix chain 'D' and resid 124 through 129 removed outlier: 4.255A pdb=" N GLU D 129 " --> pdb=" O THR D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 171 Processing helix chain 'D' and resid 174 through 183 Processing helix chain 'D' and resid 203 through 211 removed outlier: 3.970A pdb=" N PHE D 207 " --> pdb=" O ASN D 203 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU D 211 " --> pdb=" O PHE D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 221 Processing helix chain 'D' and resid 221 through 233 removed outlier: 4.050A pdb=" N THR D 227 " --> pdb=" O SER D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 249 Processing helix chain 'D' and resid 250 through 253 Processing helix chain 'D' and resid 254 through 262 removed outlier: 3.786A pdb=" N PHE D 258 " --> pdb=" O ASP D 254 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY D 262 " --> pdb=" O PHE D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 297 Processing helix chain 'D' and resid 298 through 307 Processing helix chain 'D' and resid 352 through 368 removed outlier: 4.448A pdb=" N LEU D 356 " --> pdb=" O PRO D 352 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER D 368 " --> pdb=" O ARG D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 388 Processing helix chain 'D' and resid 403 through 409 removed outlier: 3.559A pdb=" N LYS D 408 " --> pdb=" O SER D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 436 removed outlier: 3.722A pdb=" N ARG D 423 " --> pdb=" O GLU D 419 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N THR D 436 " --> pdb=" O ARG D 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 24 Processing helix chain 'E' and resid 26 through 32 removed outlier: 3.570A pdb=" N ALA E 32 " --> pdb=" O GLU E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 73 removed outlier: 3.598A pdb=" N LEU E 72 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 81 removed outlier: 3.593A pdb=" N GLN E 81 " --> pdb=" O PHE E 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 13 Processing helix chain 'G' and resid 22 through 27 removed outlier: 3.552A pdb=" N THR G 26 " --> pdb=" O ARG G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 50 through 52 No H-bonds generated for 'chain 'G' and resid 50 through 52' Processing helix chain 'G' and resid 124 through 129 removed outlier: 4.224A pdb=" N GLU G 129 " --> pdb=" O THR G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 171 Processing helix chain 'G' and resid 174 through 183 Processing helix chain 'G' and resid 203 through 211 removed outlier: 3.982A pdb=" N PHE G 207 " --> pdb=" O ASN G 203 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU G 211 " --> pdb=" O PHE G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 221 Processing helix chain 'G' and resid 221 through 233 removed outlier: 4.046A pdb=" N THR G 227 " --> pdb=" O SER G 223 " (cutoff:3.500A) Processing helix chain 'G' and resid 242 through 249 Processing helix chain 'G' and resid 250 through 253 Processing helix chain 'G' and resid 254 through 262 removed outlier: 3.698A pdb=" N PHE G 258 " --> pdb=" O ASP G 254 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY G 262 " --> pdb=" O PHE G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 297 Processing helix chain 'G' and resid 299 through 307 Processing helix chain 'G' and resid 352 through 368 removed outlier: 4.462A pdb=" N LEU G 356 " --> pdb=" O PRO G 352 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER G 368 " --> pdb=" O ARG G 364 " (cutoff:3.500A) Processing helix chain 'G' and resid 371 through 388 Processing helix chain 'G' and resid 403 through 409 removed outlier: 3.567A pdb=" N LYS G 408 " --> pdb=" O SER G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 419 through 436 removed outlier: 3.703A pdb=" N ARG G 423 " --> pdb=" O GLU G 419 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR G 436 " --> pdb=" O ARG G 432 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 24 Processing helix chain 'H' and resid 26 through 32 removed outlier: 3.598A pdb=" N ALA H 32 " --> pdb=" O GLU H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 73 removed outlier: 3.641A pdb=" N LEU H 72 " --> pdb=" O ARG H 68 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 81 removed outlier: 3.604A pdb=" N GLN H 81 " --> pdb=" O PHE H 78 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 19 through 21 Processing sheet with id=AA2, first strand: chain 'B' and resid 44 through 48 removed outlier: 5.776A pdb=" N TYR B 45 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL B 157 " --> pdb=" O TYR B 45 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY B 47 " --> pdb=" O ILE B 155 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 99 removed outlier: 4.353A pdb=" N ASP B 57 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ALA B 80 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 7.026A pdb=" N THR B 112 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 189 through 191 Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 191 removed outlier: 6.390A pdb=" N ARG B 338 " --> pdb=" O ILE B 334 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA B 327 " --> pdb=" O LYS B 322 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN B 312 " --> pdb=" O THR B 273 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 56 through 60 removed outlier: 3.529A pdb=" N LEU A 58 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N THR A 35 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 9.599A pdb=" N ARG A 140 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 10.313A pdb=" N ASP A 37 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N THR A 142 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A 39 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N LEU A 148 " --> pdb=" O PRO A 43 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N HIS A 131 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LYS A 144 " --> pdb=" O PHE A 129 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE A 129 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL A 146 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR A 127 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LEU A 148 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N VAL A 125 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 56 through 60 removed outlier: 3.529A pdb=" N LEU A 58 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N THR A 35 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 9.599A pdb=" N ARG A 140 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 10.313A pdb=" N ASP A 37 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N THR A 142 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A 39 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N LEU A 148 " --> pdb=" O PRO A 43 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N HIS A 131 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LYS A 144 " --> pdb=" O PHE A 129 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE A 129 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL A 146 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR A 127 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LEU A 148 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N VAL A 125 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ARG A 104 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N PHE A 98 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL A 106 " --> pdb=" O GLU A 96 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 19 through 21 Processing sheet with id=AB1, first strand: chain 'D' and resid 44 through 48 removed outlier: 5.795A pdb=" N TYR D 45 " --> pdb=" O VAL D 157 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL D 157 " --> pdb=" O TYR D 45 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY D 47 " --> pdb=" O ILE D 155 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 97 through 99 removed outlier: 4.344A pdb=" N ASP D 57 " --> pdb=" O ARG D 72 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ALA D 80 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 103 through 105 removed outlier: 6.990A pdb=" N THR D 112 " --> pdb=" O LEU D 120 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 189 through 191 Processing sheet with id=AB5, first strand: chain 'D' and resid 189 through 191 removed outlier: 6.349A pdb=" N ARG D 338 " --> pdb=" O ILE D 334 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA D 327 " --> pdb=" O LYS D 322 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN D 312 " --> pdb=" O THR D 273 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 56 through 60 removed outlier: 3.502A pdb=" N LEU E 58 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N THR E 35 " --> pdb=" O ARG E 140 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR E 142 " --> pdb=" O THR E 35 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ASP E 37 " --> pdb=" O THR E 142 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N LYS E 144 " --> pdb=" O ASP E 37 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N PHE E 39 " --> pdb=" O LYS E 144 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N VAL E 146 " --> pdb=" O PHE E 39 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N TRP E 41 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N LEU E 148 " --> pdb=" O TRP E 41 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N HIS E 131 " --> pdb=" O THR E 142 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LYS E 144 " --> pdb=" O PHE E 129 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE E 129 " --> pdb=" O LYS E 144 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N VAL E 146 " --> pdb=" O THR E 127 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR E 127 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LEU E 148 " --> pdb=" O VAL E 125 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N VAL E 125 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 56 through 60 removed outlier: 3.502A pdb=" N LEU E 58 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N THR E 35 " --> pdb=" O ARG E 140 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR E 142 " --> pdb=" O THR E 35 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ASP E 37 " --> pdb=" O THR E 142 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N LYS E 144 " --> pdb=" O ASP E 37 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N PHE E 39 " --> pdb=" O LYS E 144 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N VAL E 146 " --> pdb=" O PHE E 39 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N TRP E 41 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N LEU E 148 " --> pdb=" O TRP E 41 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N HIS E 131 " --> pdb=" O THR E 142 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LYS E 144 " --> pdb=" O PHE E 129 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE E 129 " --> pdb=" O LYS E 144 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N VAL E 146 " --> pdb=" O THR E 127 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR E 127 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LEU E 148 " --> pdb=" O VAL E 125 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N VAL E 125 " --> pdb=" O LEU E 148 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ARG E 104 " --> pdb=" O PHE E 98 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N PHE E 98 " --> pdb=" O ARG E 104 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL E 106 " --> pdb=" O GLU E 96 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 19 through 21 Processing sheet with id=AB9, first strand: chain 'G' and resid 44 through 48 removed outlier: 5.810A pdb=" N TYR G 45 " --> pdb=" O VAL G 157 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL G 157 " --> pdb=" O TYR G 45 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY G 47 " --> pdb=" O ILE G 155 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 97 through 99 removed outlier: 4.361A pdb=" N ASP G 57 " --> pdb=" O ARG G 72 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ALA G 80 " --> pdb=" O LEU G 145 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 103 through 105 removed outlier: 7.016A pdb=" N THR G 112 " --> pdb=" O LEU G 120 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 189 through 191 Processing sheet with id=AC4, first strand: chain 'G' and resid 189 through 191 removed outlier: 6.366A pdb=" N ARG G 338 " --> pdb=" O ILE G 334 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA G 327 " --> pdb=" O LYS G 322 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN G 312 " --> pdb=" O THR G 273 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 56 through 60 removed outlier: 3.568A pdb=" N LEU H 58 " --> pdb=" O VAL H 42 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N THR H 35 " --> pdb=" O ALA H 138 " (cutoff:3.500A) removed outlier: 9.619A pdb=" N ARG H 140 " --> pdb=" O THR H 35 " (cutoff:3.500A) removed outlier: 10.320A pdb=" N ASP H 37 " --> pdb=" O ARG H 140 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N THR H 142 " --> pdb=" O ASP H 37 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE H 39 " --> pdb=" O THR H 142 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N LEU H 148 " --> pdb=" O PRO H 43 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N HIS H 131 " --> pdb=" O THR H 142 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LYS H 144 " --> pdb=" O PHE H 129 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N PHE H 129 " --> pdb=" O LYS H 144 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL H 146 " --> pdb=" O THR H 127 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR H 127 " --> pdb=" O VAL H 146 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU H 148 " --> pdb=" O VAL H 125 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL H 125 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 56 through 60 removed outlier: 3.568A pdb=" N LEU H 58 " --> pdb=" O VAL H 42 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N THR H 35 " --> pdb=" O ALA H 138 " (cutoff:3.500A) removed outlier: 9.619A pdb=" N ARG H 140 " --> pdb=" O THR H 35 " (cutoff:3.500A) removed outlier: 10.320A pdb=" N ASP H 37 " --> pdb=" O ARG H 140 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N THR H 142 " --> pdb=" O ASP H 37 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE H 39 " --> pdb=" O THR H 142 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N LEU H 148 " --> pdb=" O PRO H 43 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N HIS H 131 " --> pdb=" O THR H 142 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LYS H 144 " --> pdb=" O PHE H 129 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N PHE H 129 " --> pdb=" O LYS H 144 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL H 146 " --> pdb=" O THR H 127 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR H 127 " --> pdb=" O VAL H 146 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU H 148 " --> pdb=" O VAL H 125 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL H 125 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ARG H 104 " --> pdb=" O PHE H 98 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE H 98 " --> pdb=" O ARG H 104 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL H 106 " --> pdb=" O GLU H 96 " (cutoff:3.500A) 707 hydrogen bonds defined for protein. 1944 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: 5.35 Time building geometry restraints manager: 4.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.42: 6505 1.42 - 1.62: 8099 1.62 - 1.81: 137 1.81 - 2.01: 1 2.01 - 2.20: 12 Bond restraints: 14754 Sorted by residual: bond pdb=" N IAC B 502 " pdb=" C IAC B 502 " ideal model delta sigma weight residual 1.363 1.331 0.032 2.00e-02 2.50e+03 2.62e+00 bond pdb=" N IAC D 502 " pdb=" C IAC D 502 " ideal model delta sigma weight residual 1.363 1.331 0.032 2.00e-02 2.50e+03 2.57e+00 bond pdb=" C7 IAC B 502 " pdb=" C8 IAC B 502 " ideal model delta sigma weight residual 1.366 1.397 -0.031 2.00e-02 2.50e+03 2.45e+00 bond pdb=" N IAC G 502 " pdb=" C IAC G 502 " ideal model delta sigma weight residual 1.363 1.332 0.031 2.00e-02 2.50e+03 2.43e+00 bond pdb=" C7 IAC D 502 " pdb=" C8 IAC D 502 " ideal model delta sigma weight residual 1.366 1.396 -0.030 2.00e-02 2.50e+03 2.32e+00 ... (remaining 14749 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 19776 2.42 - 4.84: 194 4.84 - 7.27: 19 7.27 - 9.69: 2 9.69 - 12.11: 1 Bond angle restraints: 19992 Sorted by residual: angle pdb=" CB MET D 215 " pdb=" CG MET D 215 " pdb=" SD MET D 215 " ideal model delta sigma weight residual 112.70 124.81 -12.11 3.00e+00 1.11e-01 1.63e+01 angle pdb=" N ILE G 325 " pdb=" CA ILE G 325 " pdb=" C ILE G 325 " ideal model delta sigma weight residual 113.42 108.99 4.43 1.17e+00 7.31e-01 1.44e+01 angle pdb=" N ILE B 325 " pdb=" CA ILE B 325 " pdb=" C ILE B 325 " ideal model delta sigma weight residual 113.42 108.99 4.43 1.17e+00 7.31e-01 1.43e+01 angle pdb=" N ILE D 325 " pdb=" CA ILE D 325 " pdb=" C ILE D 325 " ideal model delta sigma weight residual 113.42 109.04 4.38 1.17e+00 7.31e-01 1.40e+01 angle pdb=" C HIS B 276 " pdb=" N PHE B 277 " pdb=" CA PHE B 277 " ideal model delta sigma weight residual 121.54 128.65 -7.11 1.91e+00 2.74e-01 1.38e+01 ... (remaining 19987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 7529 16.96 - 33.91: 892 33.91 - 50.87: 235 50.87 - 67.82: 57 67.82 - 84.78: 23 Dihedral angle restraints: 8736 sinusoidal: 3567 harmonic: 5169 Sorted by residual: dihedral pdb=" CA LEU E 90 " pdb=" C LEU E 90 " pdb=" N GLN E 91 " pdb=" CA GLN E 91 " ideal model delta harmonic sigma weight residual 180.00 160.25 19.75 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA LEU A 90 " pdb=" C LEU A 90 " pdb=" N GLN A 91 " pdb=" CA GLN A 91 " ideal model delta harmonic sigma weight residual 180.00 160.30 19.70 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA LEU H 90 " pdb=" C LEU H 90 " pdb=" N GLN H 91 " pdb=" CA GLN H 91 " ideal model delta harmonic sigma weight residual 180.00 160.42 19.58 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 8733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1254 0.030 - 0.060: 527 0.060 - 0.091: 174 0.091 - 0.121: 108 0.121 - 0.151: 19 Chirality restraints: 2082 Sorted by residual: chirality pdb=" CA HIS D 216 " pdb=" N HIS D 216 " pdb=" C HIS D 216 " pdb=" CB HIS D 216 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CA ILE G 263 " pdb=" N ILE G 263 " pdb=" C ILE G 263 " pdb=" CB ILE G 263 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA HIS B 216 " pdb=" N HIS B 216 " pdb=" C HIS B 216 " pdb=" CB HIS B 216 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.63e-01 ... (remaining 2079 not shown) Planarity restraints: 2634 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU E 101 " 0.011 2.00e-02 2.50e+03 2.32e-02 5.38e+00 pdb=" CD GLU E 101 " -0.040 2.00e-02 2.50e+03 pdb=" OE1 GLU E 101 " 0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU E 101 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 277 " -0.011 2.00e-02 2.50e+03 1.73e-02 5.23e+00 pdb=" CG PHE B 277 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE B 277 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE B 277 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE B 277 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 277 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 277 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU H 101 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.02e+00 pdb=" CD GLU H 101 " 0.035 2.00e-02 2.50e+03 pdb=" OE1 GLU H 101 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU H 101 " -0.012 2.00e-02 2.50e+03 ... (remaining 2631 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 178 2.61 - 3.19: 11598 3.19 - 3.76: 22021 3.76 - 4.33: 32163 4.33 - 4.90: 53779 Nonbonded interactions: 119739 Sorted by model distance: nonbonded pdb=" OD2 ASP B 377 " pdb="FE FE B 503 " model vdw 2.043 2.260 nonbonded pdb=" OD2 ASP D 377 " pdb="FE FE D 503 " model vdw 2.043 2.260 nonbonded pdb=" OD2 ASP G 377 " pdb="FE FE G 503 " model vdw 2.043 2.260 nonbonded pdb=" OD1 ASP G 377 " pdb="FE FE G 503 " model vdw 2.055 2.260 nonbonded pdb=" OD1 ASP B 377 " pdb="FE FE B 503 " model vdw 2.058 2.260 ... (remaining 119734 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'H' } ncs_group { reference = (chain 'B' and (resid 3 through 229 or resid 231 through 437 or resid 501 throug \ h 503)) selection = (chain 'D' and (resid 3 through 229 or resid 231 through 437 or resid 501 throug \ h 503)) selection = (chain 'G' and (resid 3 through 229 or resid 231 through 437 or resid 501 throug \ h 503)) } 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=0.46 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 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: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 44.300 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14754 Z= 0.211 Angle : 0.588 12.109 19992 Z= 0.320 Chirality : 0.043 0.151 2082 Planarity : 0.005 0.043 2634 Dihedral : 16.316 84.781 5412 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.00 % Favored : 96.88 % Rotamer: Outliers : 1.52 % Allowed : 21.54 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.43 (0.20), residues: 1773 helix: 0.78 (0.23), residues: 549 sheet: 0.66 (0.29), residues: 309 loop : -0.05 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 429 HIS 0.004 0.001 HIS B 216 PHE 0.039 0.001 PHE B 277 TYR 0.013 0.001 TYR G 426 ARG 0.004 0.000 ARG D 146 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 1.620 Fit side-chains REVERT: B 437 MET cc_start: 0.7673 (mmt) cc_final: 0.7446 (mmt) REVERT: D 209 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7984 (mt-10) REVERT: D 255 TYR cc_start: 0.8111 (m-10) cc_final: 0.7725 (m-10) outliers start: 23 outliers final: 21 residues processed: 188 average time/residue: 1.5558 time to fit residues: 317.4916 Evaluate side-chains 184 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain D residue 9 ASP Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 35 GLN Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain G residue 436 THR Chi-restraints excluded: chain H residue 116 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 158 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN A 97 GLN E 97 GLN H 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.103993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.082182 restraints weight = 49209.663| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.46 r_work: 0.2844 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.0686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14754 Z= 0.275 Angle : 0.573 8.803 19992 Z= 0.307 Chirality : 0.044 0.159 2082 Planarity : 0.005 0.047 2634 Dihedral : 6.097 58.508 2028 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.34 % Favored : 96.54 % Rotamer: Outliers : 2.37 % Allowed : 19.96 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.50 (0.20), residues: 1773 helix: 0.95 (0.23), residues: 552 sheet: 0.29 (0.28), residues: 336 loop : 0.07 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 429 HIS 0.005 0.001 HIS G 311 PHE 0.032 0.002 PHE B 277 TYR 0.014 0.001 TYR D 426 ARG 0.004 0.000 ARG G 146 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 174 time to evaluate : 1.608 Fit side-chains revert: symmetry clash REVERT: B 437 MET cc_start: 0.7725 (mmt) cc_final: 0.7499 (mmt) REVERT: D 209 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8107 (mp0) REVERT: G 19 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7473 (ptt-90) REVERT: G 34 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7173 (mt-10) REVERT: G 338 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7565 (ttt-90) REVERT: H 49 GLU cc_start: 0.8194 (tp30) cc_final: 0.7985 (tp30) outliers start: 36 outliers final: 7 residues processed: 197 average time/residue: 1.6850 time to fit residues: 357.9820 Evaluate side-chains 175 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 165 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 361 MET Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain G residue 3 SER Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 338 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 122 optimal weight: 6.9990 chunk 120 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN B 304 GLN A 97 GLN E 97 GLN H 97 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.102378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.080141 restraints weight = 59568.871| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.76 r_work: 0.2801 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 14754 Z= 0.411 Angle : 0.633 10.985 19992 Z= 0.339 Chirality : 0.047 0.175 2082 Planarity : 0.005 0.048 2634 Dihedral : 5.524 56.816 1998 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.68 % Favored : 96.20 % Rotamer: Outliers : 2.11 % Allowed : 20.36 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.36 (0.20), residues: 1773 helix: 0.83 (0.23), residues: 552 sheet: 0.42 (0.29), residues: 306 loop : -0.09 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 429 HIS 0.006 0.001 HIS G 311 PHE 0.032 0.002 PHE B 277 TYR 0.016 0.002 TYR D 426 ARG 0.005 0.000 ARG G 146 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 1.599 Fit side-chains revert: symmetry clash REVERT: B 180 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8323 (ttp) REVERT: B 338 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7903 (ttt-90) REVERT: B 437 MET cc_start: 0.7592 (mmt) cc_final: 0.7331 (mmt) REVERT: A 120 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8238 (mm-30) REVERT: D 52 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8481 (pp) REVERT: D 209 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7122 (mp0) REVERT: D 437 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.6708 (mmm) REVERT: G 19 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7434 (ptt-90) REVERT: G 338 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7568 (ttt-90) REVERT: H 49 GLU cc_start: 0.8318 (tp30) cc_final: 0.8078 (tp30) outliers start: 32 outliers final: 10 residues processed: 180 average time/residue: 1.6830 time to fit residues: 326.9274 Evaluate side-chains 178 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 338 ARG Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 361 MET Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain D residue 437 MET Chi-restraints excluded: chain G residue 3 SER Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 338 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 26 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN A 97 GLN E 97 GLN H 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.103625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.081878 restraints weight = 49973.822| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.50 r_work: 0.2839 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.0822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14754 Z= 0.272 Angle : 0.569 10.251 19992 Z= 0.305 Chirality : 0.044 0.160 2082 Planarity : 0.005 0.046 2634 Dihedral : 5.266 52.466 1995 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.63 % Favored : 96.20 % Rotamer: Outliers : 2.37 % Allowed : 19.76 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.41 (0.20), residues: 1773 helix: 0.98 (0.23), residues: 552 sheet: 0.23 (0.28), residues: 336 loop : -0.05 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 429 HIS 0.004 0.001 HIS G 311 PHE 0.034 0.002 PHE B 277 TYR 0.013 0.001 TYR D 426 ARG 0.004 0.000 ARG G 146 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 1.750 Fit side-chains revert: symmetry clash REVERT: B 180 MET cc_start: 0.8988 (OUTLIER) cc_final: 0.8240 (ttp) REVERT: B 338 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7911 (ttt-90) REVERT: B 437 MET cc_start: 0.7632 (mmt) cc_final: 0.7407 (mmt) REVERT: A 120 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8255 (mm-30) REVERT: D 209 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7377 (mp0) REVERT: D 437 MET cc_start: 0.7437 (OUTLIER) cc_final: 0.6782 (mmm) REVERT: G 19 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7454 (ptt-90) REVERT: G 338 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7504 (ttt-90) REVERT: H 49 GLU cc_start: 0.8311 (tp30) cc_final: 0.8036 (tp30) REVERT: H 96 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7967 (mt-10) outliers start: 36 outliers final: 12 residues processed: 188 average time/residue: 1.6540 time to fit residues: 335.8141 Evaluate side-chains 183 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 338 ARG Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 361 MET Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain D residue 437 MET Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain G residue 3 SER Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 338 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 124 optimal weight: 0.6980 chunk 116 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 143 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN A 97 GLN E 97 GLN H 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.106472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.084507 restraints weight = 57301.290| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.74 r_work: 0.2877 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14754 Z= 0.157 Angle : 0.526 10.638 19992 Z= 0.279 Chirality : 0.042 0.157 2082 Planarity : 0.004 0.044 2634 Dihedral : 4.950 48.846 1995 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.46 % Favored : 96.37 % Rotamer: Outliers : 1.65 % Allowed : 20.75 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.66 (0.20), residues: 1773 helix: 1.21 (0.23), residues: 552 sheet: 0.26 (0.28), residues: 336 loop : 0.13 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 429 HIS 0.003 0.001 HIS B 216 PHE 0.034 0.001 PHE B 277 TYR 0.008 0.001 TYR B 45 ARG 0.004 0.000 ARG G 146 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 180 time to evaluate : 1.810 Fit side-chains REVERT: B 180 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8111 (ttp) REVERT: B 338 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7873 (ttt-90) REVERT: B 437 MET cc_start: 0.7684 (mmt) cc_final: 0.7398 (mmt) REVERT: A 120 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8274 (mm-30) REVERT: G 338 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7535 (ttt-90) REVERT: H 49 GLU cc_start: 0.8324 (tp30) cc_final: 0.8020 (tp30) outliers start: 25 outliers final: 7 residues processed: 191 average time/residue: 1.6187 time to fit residues: 334.5477 Evaluate side-chains 176 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 165 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 338 ARG Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 338 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 54 optimal weight: 7.9990 chunk 161 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 156 optimal weight: 7.9990 chunk 109 optimal weight: 0.7980 chunk 87 optimal weight: 0.0970 chunk 140 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 59 optimal weight: 0.4980 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN A 97 GLN E 97 GLN H 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.105219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.083791 restraints weight = 44411.921| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.34 r_work: 0.2897 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14754 Z= 0.168 Angle : 0.532 10.982 19992 Z= 0.279 Chirality : 0.042 0.144 2082 Planarity : 0.004 0.043 2634 Dihedral : 4.565 43.763 1992 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.51 % Favored : 96.32 % Rotamer: Outliers : 1.65 % Allowed : 21.34 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.83 (0.20), residues: 1773 helix: 1.26 (0.23), residues: 555 sheet: 0.45 (0.29), residues: 306 loop : 0.26 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 429 HIS 0.003 0.001 HIS B 216 PHE 0.031 0.001 PHE B 277 TYR 0.009 0.001 TYR B 45 ARG 0.004 0.000 ARG B 146 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 1.594 Fit side-chains REVERT: B 338 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7843 (ttt-90) REVERT: B 437 MET cc_start: 0.7693 (mmt) cc_final: 0.7358 (mmt) REVERT: A 120 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8275 (mm-30) REVERT: D 210 ASN cc_start: 0.8635 (t0) cc_final: 0.8316 (t0) REVERT: G 19 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7493 (ptt-90) REVERT: G 338 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7492 (ttt-90) REVERT: H 49 GLU cc_start: 0.8304 (tp30) cc_final: 0.7994 (tp30) outliers start: 25 outliers final: 7 residues processed: 190 average time/residue: 1.5974 time to fit residues: 328.6797 Evaluate side-chains 176 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 165 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 338 ARG Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 338 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.2921 > 50: distance: 42 - 46: 5.145 distance: 46 - 47: 15.349 distance: 47 - 48: 12.281 distance: 47 - 50: 31.488 distance: 48 - 49: 10.755 distance: 48 - 58: 3.977 distance: 50 - 51: 12.362 distance: 51 - 52: 18.859 distance: 51 - 53: 34.556 distance: 52 - 54: 6.242 distance: 53 - 55: 8.540 distance: 54 - 56: 29.360 distance: 55 - 56: 20.290 distance: 56 - 57: 15.206 distance: 58 - 59: 15.661 distance: 59 - 60: 11.639 distance: 59 - 62: 14.748 distance: 60 - 61: 4.816 distance: 60 - 66: 14.838 distance: 61 - 79: 22.430 distance: 62 - 63: 27.119 distance: 63 - 64: 17.101 distance: 63 - 65: 8.822 distance: 66 - 67: 21.858 distance: 66 - 72: 8.175 distance: 67 - 68: 29.956 distance: 67 - 70: 13.383 distance: 68 - 69: 13.993 distance: 68 - 73: 4.144 distance: 69 - 88: 21.211 distance: 70 - 71: 26.784 distance: 71 - 72: 7.403 distance: 73 - 74: 7.215 distance: 74 - 75: 29.567 distance: 74 - 77: 11.721 distance: 75 - 76: 18.325 distance: 75 - 79: 30.917 distance: 77 - 78: 47.831 distance: 79 - 80: 11.843 distance: 80 - 81: 5.717 distance: 80 - 83: 11.651 distance: 81 - 82: 5.907 distance: 81 - 88: 8.079 distance: 82 - 101: 31.957 distance: 83 - 84: 11.568 distance: 84 - 85: 7.421 distance: 85 - 86: 6.334 distance: 85 - 87: 4.682 distance: 88 - 89: 10.969 distance: 89 - 90: 4.298 distance: 89 - 92: 22.975 distance: 90 - 91: 25.730 distance: 90 - 96: 24.945 distance: 92 - 93: 21.628 distance: 93 - 94: 12.116 distance: 93 - 95: 15.925 distance: 96 - 97: 11.371 distance: 97 - 98: 10.119 distance: 97 - 100: 29.379 distance: 98 - 99: 18.609 distance: 98 - 101: 22.302 distance: 101 - 102: 14.251 distance: 102 - 103: 10.226 distance: 103 - 104: 13.669 distance: 103 - 105: 7.211 distance: 105 - 106: 17.208 distance: 106 - 107: 13.696 distance: 107 - 108: 15.057 distance: 107 - 109: 24.739 distance: 109 - 110: 12.325 distance: 110 - 111: 11.268 distance: 110 - 113: 11.249 distance: 111 - 112: 7.735 distance: 113 - 114: 14.766 distance: 114 - 115: 7.289 distance: 115 - 116: 9.337 distance: 115 - 117: 3.632