Starting phenix.real_space_refine on Thu Sep 26 21:56:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h2t_34443/09_2024/8h2t_34443.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h2t_34443/09_2024/8h2t_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h2t_34443/09_2024/8h2t_34443.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h2t_34443/09_2024/8h2t_34443.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h2t_34443/09_2024/8h2t_34443.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h2t_34443/09_2024/8h2t_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 12.28, per 1000 atoms: 0.85 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: 3.36 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: 1.94 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: 5.14 Time building geometry restraints manager: 3.94 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: 0.00 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: 0.590 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: 0.510 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 42.450 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.910 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 23 poor density : 166 time to evaluate : 1.733 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: 1.5104 time to fit residues: 307.7205 Evaluate side-chains 184 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 162 time to evaluate : 1.457 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 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 fitting. rotamer outliers: 36 poor density : 174 time to evaluate : 1.578 Fit side-chains revert: symmetry clash REVERT: B 437 MET cc_start: 0.7695 (mmt) cc_final: 0.7460 (mmt) REVERT: D 209 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8096 (mp0) REVERT: G 19 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7473 (ptt-90) REVERT: G 34 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7195 (mt-10) REVERT: G 338 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7228 (ttt-90) REVERT: H 49 GLU cc_start: 0.7969 (tp30) cc_final: 0.7763 (tp30) outliers start: 36 outliers final: 7 residues processed: 197 average time/residue: 1.6998 time to fit residues: 361.7682 Evaluate side-chains 175 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 165 time to evaluate : 1.601 ------------------------------------------------------------------------------- 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 87 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 131 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 171 optimal weight: 0.4980 chunk 140 optimal weight: 5.9990 chunk 156 optimal weight: 0.0870 chunk 53 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 overall best weight: 1.5164 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 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 : 0.003 0.030 14754 Z= 0.173 Angle : 0.527 9.964 19992 Z= 0.280 Chirality : 0.042 0.144 2082 Planarity : 0.004 0.046 2634 Dihedral : 5.018 49.400 1998 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.12 % Favored : 96.77 % Rotamer: Outliers : 1.84 % Allowed : 20.36 % Favored : 77.80 % 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: 0.68 (0.20), residues: 1773 helix: 1.17 (0.23), residues: 552 sheet: 0.31 (0.28), residues: 336 loop : 0.17 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 429 HIS 0.003 0.001 HIS B 216 PHE 0.030 0.001 PHE B 277 TYR 0.009 0.001 TYR D 426 ARG 0.004 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 207 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 179 time to evaluate : 1.617 Fit side-chains REVERT: B 180 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8102 (ttp) REVERT: B 437 MET cc_start: 0.7718 (mmt) cc_final: 0.7357 (mmt) REVERT: A 120 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7899 (mm-30) REVERT: D 210 ASN cc_start: 0.8598 (t0) cc_final: 0.8267 (t0) REVERT: G 34 GLU cc_start: 0.7215 (mt-10) cc_final: 0.6811 (pt0) REVERT: G 338 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7163 (ttt-90) outliers start: 28 outliers final: 5 residues processed: 195 average time/residue: 1.6255 time to fit residues: 342.8924 Evaluate side-chains 173 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 165 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 180 MET 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 8.9990 chunk 119 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 17 optimal weight: 8.9990 chunk 75 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 158 optimal weight: 0.9990 chunk 168 optimal weight: 10.0000 chunk 150 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 overall best weight: 1.1988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14754 Z= 0.150 Angle : 0.509 10.494 19992 Z= 0.269 Chirality : 0.042 0.144 2082 Planarity : 0.004 0.044 2634 Dihedral : 4.460 40.137 1992 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.34 % Favored : 96.49 % Rotamer: Outliers : 1.98 % Allowed : 20.82 % Favored : 77.21 % 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: 0.81 (0.20), residues: 1773 helix: 1.30 (0.23), residues: 555 sheet: 0.30 (0.27), residues: 339 loop : 0.27 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 429 HIS 0.003 0.001 HIS B 216 PHE 0.031 0.001 PHE B 277 TYR 0.008 0.001 TYR B 45 ARG 0.003 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 204 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 174 time to evaluate : 1.614 Fit side-chains REVERT: B 437 MET cc_start: 0.7752 (mmt) cc_final: 0.7360 (mmt) REVERT: A 66 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7893 (mt-10) REVERT: A 120 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7891 (mm-30) REVERT: D 210 ASN cc_start: 0.8580 (t0) cc_final: 0.8272 (t0) REVERT: G 19 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7516 (ptt-90) REVERT: G 34 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6860 (pt0) REVERT: G 338 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7181 (ttt-90) REVERT: H 159 GLN cc_start: 0.9151 (OUTLIER) cc_final: 0.8932 (mt0) outliers start: 30 outliers final: 7 residues processed: 189 average time/residue: 1.5387 time to fit residues: 314.4934 Evaluate side-chains 178 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 167 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain G residue 3 SER 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 Chi-restraints excluded: chain H residue 159 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 125 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 chunk 143 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 56 optimal weight: 8.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 14754 Z= 0.376 Angle : 0.617 11.344 19992 Z= 0.327 Chirality : 0.047 0.176 2082 Planarity : 0.005 0.049 2634 Dihedral : 4.976 43.781 1992 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.91 % Favored : 95.92 % Rotamer: Outliers : 2.37 % Allowed : 20.55 % Favored : 77.08 % 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: 0.57 (0.20), residues: 1773 helix: 1.01 (0.22), residues: 555 sheet: 0.44 (0.29), residues: 306 loop : 0.07 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 429 HIS 0.006 0.001 HIS G 311 PHE 0.035 0.002 PHE B 277 TYR 0.016 0.002 TYR B 426 ARG 0.005 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 204 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 168 time to evaluate : 1.525 Fit side-chains REVERT: B 180 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8579 (ttt) REVERT: B 437 MET cc_start: 0.7632 (mmt) cc_final: 0.7382 (mmt) REVERT: A 120 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7914 (mm-30) REVERT: D 52 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8429 (pp) REVERT: D 437 MET cc_start: 0.7304 (OUTLIER) cc_final: 0.6578 (mmm) REVERT: G 19 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7445 (ptt-90) REVERT: G 338 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7210 (ttt-90) outliers start: 36 outliers final: 11 residues processed: 189 average time/residue: 1.6259 time to fit residues: 332.0417 Evaluate side-chains 180 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 163 time to evaluate : 1.598 ------------------------------------------------------------------------------- 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 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 52 LEU Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 437 MET Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain G residue 3 SER Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain H residue 116 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 168 optimal weight: 9.9990 chunk 139 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 162 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 14754 Z= 0.439 Angle : 0.652 12.353 19992 Z= 0.347 Chirality : 0.048 0.182 2082 Planarity : 0.005 0.049 2634 Dihedral : 5.180 45.663 1992 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.02 % Favored : 95.80 % Rotamer: Outliers : 2.24 % Allowed : 20.49 % Favored : 77.27 % 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: 0.37 (0.20), residues: 1773 helix: 0.85 (0.22), residues: 555 sheet: 0.42 (0.29), residues: 306 loop : -0.10 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 429 HIS 0.006 0.001 HIS G 311 PHE 0.035 0.002 PHE B 277 TYR 0.014 0.002 TYR G 25 ARG 0.005 0.000 ARG G 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 fitting. rotamer outliers: 34 poor density : 166 time to evaluate : 1.680 Fit side-chains REVERT: B 180 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8302 (ttp) REVERT: B 308 MET cc_start: 0.7081 (mtp) cc_final: 0.6734 (ttt) REVERT: B 437 MET cc_start: 0.7537 (mmt) cc_final: 0.7295 (mmt) REVERT: A 120 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7918 (mm-30) REVERT: D 437 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.7013 (mmp) REVERT: G 19 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7424 (ptt-90) REVERT: G 338 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7243 (ttt-90) REVERT: H 49 GLU cc_start: 0.8096 (tp30) cc_final: 0.7829 (tp30) outliers start: 34 outliers final: 13 residues processed: 186 average time/residue: 1.5473 time to fit residues: 311.3763 Evaluate side-chains 178 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 160 time to evaluate : 1.684 ------------------------------------------------------------------------------- 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 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 15 VAL Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 437 MET Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain G residue 3 SER Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain H residue 116 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 141 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14754 Z= 0.246 Angle : 0.578 12.049 19992 Z= 0.306 Chirality : 0.044 0.157 2082 Planarity : 0.004 0.048 2634 Dihedral : 4.929 47.225 1992 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.57 % Favored : 96.26 % Rotamer: Outliers : 1.32 % Allowed : 21.54 % Favored : 77.14 % 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: 0.54 (0.20), residues: 1773 helix: 1.02 (0.23), residues: 555 sheet: 0.42 (0.29), residues: 306 loop : 0.03 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 429 HIS 0.004 0.001 HIS A 112 PHE 0.032 0.002 PHE B 277 TYR 0.011 0.001 TYR B 45 ARG 0.004 0.000 ARG D 146 *********************** REFINEMENT MACRO_CYCLE 7 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 197 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 177 time to evaluate : 1.811 Fit side-chains revert: symmetry clash REVERT: B 180 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8223 (ttp) REVERT: B 308 MET cc_start: 0.6910 (mtp) cc_final: 0.6637 (ttt) REVERT: B 422 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.7052 (mmt) REVERT: B 437 MET cc_start: 0.7623 (mmt) cc_final: 0.7355 (mmt) REVERT: A 120 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7908 (mm-30) REVERT: D 437 MET cc_start: 0.7205 (OUTLIER) cc_final: 0.6866 (mmp) REVERT: G 19 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7471 (ptt-90) REVERT: G 34 GLU cc_start: 0.7313 (mt-10) cc_final: 0.7107 (pt0) REVERT: G 338 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7212 (ttt-90) REVERT: H 49 GLU cc_start: 0.8081 (tp30) cc_final: 0.7796 (tp30) outliers start: 20 outliers final: 11 residues processed: 190 average time/residue: 1.5288 time to fit residues: 314.6187 Evaluate side-chains 186 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 169 time to evaluate : 1.646 ------------------------------------------------------------------------------- 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 407 LEU Chi-restraints excluded: chain B residue 422 MET 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 263 ILE Chi-restraints excluded: chain D residue 437 MET Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain G residue 3 SER Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain H residue 116 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 7.9990 chunk 50 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 106 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 131 optimal weight: 0.9980 chunk 152 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 146 optimal weight: 7.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14754 Z= 0.217 Angle : 0.565 10.940 19992 Z= 0.298 Chirality : 0.043 0.151 2082 Planarity : 0.004 0.047 2634 Dihedral : 4.807 46.474 1992 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.80 % Favored : 96.03 % Rotamer: Outliers : 1.58 % Allowed : 21.87 % Favored : 76.55 % 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: 0.67 (0.20), residues: 1773 helix: 1.13 (0.23), residues: 555 sheet: 0.45 (0.29), residues: 306 loop : 0.12 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 429 HIS 0.004 0.001 HIS A 112 PHE 0.031 0.001 PHE B 277 TYR 0.010 0.001 TYR B 45 ARG 0.004 0.000 ARG D 146 *********************** REFINEMENT MACRO_CYCLE 8 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 195 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 171 time to evaluate : 1.613 Fit side-chains REVERT: B 180 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8206 (ttp) REVERT: B 308 MET cc_start: 0.6913 (mtp) cc_final: 0.6674 (ttt) REVERT: B 437 MET cc_start: 0.7641 (mmt) cc_final: 0.7376 (mmt) REVERT: A 120 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7905 (mm-30) REVERT: D 437 MET cc_start: 0.7170 (OUTLIER) cc_final: 0.6436 (mmm) REVERT: G 19 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7479 (ptt-90) REVERT: G 338 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7174 (ttt-90) REVERT: H 49 GLU cc_start: 0.8098 (tp30) cc_final: 0.7791 (tp30) outliers start: 24 outliers final: 12 residues processed: 185 average time/residue: 1.5853 time to fit residues: 316.9641 Evaluate side-chains 179 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 162 time to evaluate : 1.582 ------------------------------------------------------------------------------- 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 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 263 ILE Chi-restraints excluded: chain D residue 361 MET Chi-restraints excluded: chain D residue 437 MET Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain G residue 3 SER Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain H residue 116 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 147 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 165 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14754 Z= 0.194 Angle : 0.564 12.491 19992 Z= 0.294 Chirality : 0.043 0.179 2082 Planarity : 0.004 0.046 2634 Dihedral : 4.714 45.924 1992 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.51 % Favored : 96.32 % Rotamer: Outliers : 1.65 % Allowed : 21.81 % Favored : 76.55 % 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: 0.77 (0.20), residues: 1773 helix: 1.21 (0.23), residues: 555 sheet: 0.47 (0.29), residues: 306 loop : 0.20 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 429 HIS 0.003 0.001 HIS B 216 PHE 0.030 0.001 PHE B 277 TYR 0.010 0.001 TYR G 25 ARG 0.004 0.000 ARG D 146 *********************** REFINEMENT MACRO_CYCLE 9 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 195 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 170 time to evaluate : 1.626 Fit side-chains REVERT: B 437 MET cc_start: 0.7636 (mmt) cc_final: 0.7391 (mmt) REVERT: A 120 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7917 (mm-30) REVERT: D 210 ASN cc_start: 0.8585 (t0) cc_final: 0.8249 (t0) REVERT: D 437 MET cc_start: 0.7170 (OUTLIER) cc_final: 0.6406 (mmm) REVERT: G 19 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7494 (ptt-90) REVERT: G 338 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7165 (ttt-90) REVERT: G 422 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.6211 (mmt) REVERT: H 49 GLU cc_start: 0.8090 (tp30) cc_final: 0.7779 (tp30) outliers start: 25 outliers final: 10 residues processed: 186 average time/residue: 1.4475 time to fit residues: 292.2346 Evaluate side-chains 179 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 164 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 320 THR 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 437 MET Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain G residue 3 SER Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain G residue 422 MET Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain H residue 141 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 114 optimal weight: 8.9990 chunk 173 optimal weight: 10.0000 chunk 159 optimal weight: 4.9990 chunk 138 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 147 optimal weight: 7.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14754 Z= 0.224 Angle : 0.581 12.337 19992 Z= 0.305 Chirality : 0.044 0.185 2082 Planarity : 0.004 0.046 2634 Dihedral : 4.756 45.526 1992 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.85 % Favored : 95.98 % Rotamer: Outliers : 1.05 % Allowed : 22.40 % Favored : 76.55 % 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: 0.74 (0.20), residues: 1773 helix: 1.17 (0.23), residues: 555 sheet: 0.47 (0.29), residues: 306 loop : 0.18 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 429 HIS 0.004 0.001 HIS G 311 PHE 0.037 0.001 PHE B 277 TYR 0.010 0.001 TYR G 128 ARG 0.004 0.000 ARG G 146 ********************** REFINEMENT MACRO_CYCLE 10 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 179 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 163 time to evaluate : 1.631 Fit side-chains REVERT: B 437 MET cc_start: 0.7635 (mmt) cc_final: 0.7371 (mmt) REVERT: A 120 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7920 (mm-30) REVERT: D 437 MET cc_start: 0.7190 (OUTLIER) cc_final: 0.6826 (mmp) REVERT: G 19 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7483 (ptt-90) REVERT: G 338 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7166 (ttt-90) REVERT: H 49 GLU cc_start: 0.8102 (tp30) cc_final: 0.7789 (tp30) outliers start: 16 outliers final: 9 residues processed: 174 average time/residue: 1.4663 time to fit residues: 276.2832 Evaluate side-chains 172 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 159 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 320 THR 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 437 MET Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain G residue 3 SER Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain G residue 437 MET Chi-restraints excluded: chain H residue 116 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 0.8980 chunk 127 optimal weight: 0.0970 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 138 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 121 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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 = 0.3362 r_free = 0.3362 target = 0.105983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.084633 restraints weight = 43786.620| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.29 r_work: 0.2890 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14754 Z= 0.195 Angle : 0.564 12.033 19992 Z= 0.297 Chirality : 0.043 0.175 2082 Planarity : 0.004 0.045 2634 Dihedral : 4.700 45.260 1992 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.68 % Favored : 96.15 % Rotamer: Outliers : 0.86 % Allowed : 22.60 % Favored : 76.55 % 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: 0.79 (0.20), residues: 1773 helix: 1.22 (0.23), residues: 555 sheet: 0.48 (0.29), residues: 306 loop : 0.22 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 429 HIS 0.003 0.001 HIS B 216 PHE 0.035 0.001 PHE B 277 TYR 0.020 0.001 TYR B 426 ARG 0.004 0.000 ARG G 146 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5193.63 seconds wall clock time: 94 minutes 28.59 seconds (5668.59 seconds total)