Starting phenix.real_space_refine on Thu Sep 18 16:46:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9og0_70448/09_2025/9og0_70448.cif Found real_map, /net/cci-nas-00/data/ceres_data/9og0_70448/09_2025/9og0_70448.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9og0_70448/09_2025/9og0_70448.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9og0_70448/09_2025/9og0_70448.map" model { file = "/net/cci-nas-00/data/ceres_data/9og0_70448/09_2025/9og0_70448.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9og0_70448/09_2025/9og0_70448.cif" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 11520 2.51 5 N 3044 2.21 5 O 3292 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17976 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2166 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 7, 'TRANS': 257} Chain: "B" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2166 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 7, 'TRANS': 257} Chain: "C" Number of atoms: 4792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4792 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 10, 'TRANS': 596} Chain: "D" Number of atoms: 4792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4792 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 10, 'TRANS': 596} Chain: "E" Number of atoms: 2030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2030 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 20, 'TRANS': 231} Chain breaks: 1 Chain: "F" Number of atoms: 2030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2030 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 20, 'TRANS': 231} Chain breaks: 1 Time building chain proxies: 4.37, per 1000 atoms: 0.24 Number of scatterers: 17976 At special positions: 0 Unit cell: (161.696, 155.828, 136.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 3292 8.00 N 3044 7.00 C 11520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS C 123 " - pdb=" SG CYS C 149 " distance=2.02 Simple disulfide: pdb=" SG CYS C 137 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 307 " - pdb=" SG CYS C 535 " distance=2.03 Simple disulfide: pdb=" SG CYS D 123 " - pdb=" SG CYS D 149 " distance=2.02 Simple disulfide: pdb=" SG CYS D 137 " - pdb=" SG CYS D 164 " distance=2.03 Simple disulfide: pdb=" SG CYS D 307 " - pdb=" SG CYS D 535 " distance=2.03 Simple disulfide: pdb=" SG CYS E 73 " - pdb=" SG CYS E 246 " distance=2.03 Simple disulfide: pdb=" SG CYS E 110 " - pdb=" SG CYS E 123 " distance=2.03 Simple disulfide: pdb=" SG CYS E 181 " - pdb=" SG CYS E 216 " distance=2.03 Simple disulfide: pdb=" SG CYS E 196 " - pdb=" SG CYS E 228 " distance=2.03 Simple disulfide: pdb=" SG CYS F 73 " - pdb=" SG CYS F 246 " distance=2.03 Simple disulfide: pdb=" SG CYS F 110 " - pdb=" SG CYS F 123 " distance=2.03 Simple disulfide: pdb=" SG CYS F 181 " - pdb=" SG CYS F 216 " distance=2.03 Simple disulfide: pdb=" SG CYS F 196 " - pdb=" SG CYS F 228 " distance=2.03 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: 1.70 Conformation dependent library (CDL) restraints added in 832.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4156 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 8 sheets defined 68.2% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 1 through 26 Processing helix chain 'A' and resid 29 through 39 removed outlier: 3.791A pdb=" N VAL A 33 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 66 removed outlier: 3.633A pdb=" N MET A 43 " --> pdb=" O SER A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 94 Processing helix chain 'A' and resid 100 through 130 removed outlier: 3.959A pdb=" N ARG A 129 " --> pdb=" O ASP A 125 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER A 130 " --> pdb=" O PHE A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 166 Processing helix chain 'A' and resid 170 through 201 removed outlier: 4.059A pdb=" N PHE A 174 " --> pdb=" O VAL A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 238 removed outlier: 3.866A pdb=" N ALA A 209 " --> pdb=" O TRP A 205 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N TYR A 211 " --> pdb=" O ASN A 207 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N HIS A 238 " --> pdb=" O MET A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 265 Processing helix chain 'B' and resid 2 through 26 Processing helix chain 'B' and resid 29 through 39 removed outlier: 3.792A pdb=" N VAL B 33 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 66 removed outlier: 3.633A pdb=" N MET B 43 " --> pdb=" O SER B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 94 Processing helix chain 'B' and resid 100 through 130 removed outlier: 3.959A pdb=" N ARG B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER B 130 " --> pdb=" O PHE B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 166 Processing helix chain 'B' and resid 170 through 201 removed outlier: 4.059A pdb=" N PHE B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 238 removed outlier: 3.866A pdb=" N ALA B 209 " --> pdb=" O TRP B 205 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 210 " --> pdb=" O ASP B 206 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N TYR B 211 " --> pdb=" O ASN B 207 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS B 238 " --> pdb=" O MET B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 265 Processing helix chain 'C' and resid 154 through 159 removed outlier: 3.732A pdb=" N ASP C 158 " --> pdb=" O ASP C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 193 Processing helix chain 'C' and resid 195 through 209 Processing helix chain 'C' and resid 214 through 228 removed outlier: 3.839A pdb=" N LEU C 218 " --> pdb=" O HIS C 214 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE C 227 " --> pdb=" O TYR C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 249 Processing helix chain 'C' and resid 250 through 264 Processing helix chain 'C' and resid 272 through 285 Processing helix chain 'C' and resid 287 through 299 Processing helix chain 'C' and resid 306 through 329 removed outlier: 4.106A pdb=" N ALA C 310 " --> pdb=" O SER C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 344 Processing helix chain 'C' and resid 353 through 367 Processing helix chain 'C' and resid 368 through 382 Processing helix chain 'C' and resid 389 through 402 Processing helix chain 'C' and resid 405 through 419 removed outlier: 3.641A pdb=" N MET C 409 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 440 removed outlier: 3.921A pdb=" N MET C 440 " --> pdb=" O LYS C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 456 Processing helix chain 'C' and resid 462 through 476 removed outlier: 3.594A pdb=" N GLN C 476 " --> pdb=" O LYS C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 492 Processing helix chain 'C' and resid 498 through 513 removed outlier: 3.644A pdb=" N ALA C 502 " --> pdb=" O ASP C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 528 removed outlier: 3.733A pdb=" N PHE C 518 " --> pdb=" O HIS C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 547 removed outlier: 3.784A pdb=" N ALA C 538 " --> pdb=" O SER C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 552 removed outlier: 6.358A pdb=" N TRP C 551 " --> pdb=" O ARG C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 564 removed outlier: 3.703A pdb=" N THR C 557 " --> pdb=" O GLU C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 580 Processing helix chain 'C' and resid 582 through 595 removed outlier: 3.781A pdb=" N GLN C 586 " --> pdb=" O TYR C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 619 removed outlier: 3.609A pdb=" N ARG C 609 " --> pdb=" O GLU C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 636 Processing helix chain 'C' and resid 642 through 658 Processing helix chain 'C' and resid 659 through 673 Processing helix chain 'C' and resid 679 through 694 removed outlier: 3.590A pdb=" N SER C 694 " --> pdb=" O ALA C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 720 Processing helix chain 'D' and resid 154 through 159 removed outlier: 3.732A pdb=" N ASP D 158 " --> pdb=" O ASP D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 193 Processing helix chain 'D' and resid 195 through 209 Processing helix chain 'D' and resid 214 through 228 removed outlier: 3.839A pdb=" N LEU D 218 " --> pdb=" O HIS D 214 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE D 227 " --> pdb=" O TYR D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 249 Processing helix chain 'D' and resid 250 through 264 Processing helix chain 'D' and resid 272 through 285 Processing helix chain 'D' and resid 287 through 299 Processing helix chain 'D' and resid 306 through 329 removed outlier: 4.105A pdb=" N ALA D 310 " --> pdb=" O SER D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 344 Processing helix chain 'D' and resid 353 through 367 Processing helix chain 'D' and resid 368 through 382 Processing helix chain 'D' and resid 389 through 402 Processing helix chain 'D' and resid 405 through 419 removed outlier: 3.642A pdb=" N MET D 409 " --> pdb=" O ASN D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 440 removed outlier: 3.920A pdb=" N MET D 440 " --> pdb=" O LYS D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 456 Processing helix chain 'D' and resid 462 through 476 removed outlier: 3.595A pdb=" N GLN D 476 " --> pdb=" O LYS D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 492 Processing helix chain 'D' and resid 498 through 513 removed outlier: 3.646A pdb=" N ALA D 502 " --> pdb=" O ASP D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 528 removed outlier: 3.733A pdb=" N PHE D 518 " --> pdb=" O HIS D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 534 through 547 removed outlier: 3.784A pdb=" N ALA D 538 " --> pdb=" O SER D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 552 removed outlier: 6.358A pdb=" N TRP D 551 " --> pdb=" O ARG D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 564 removed outlier: 3.704A pdb=" N THR D 557 " --> pdb=" O GLU D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 580 Processing helix chain 'D' and resid 582 through 595 removed outlier: 3.782A pdb=" N GLN D 586 " --> pdb=" O TYR D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 619 removed outlier: 3.609A pdb=" N ARG D 609 " --> pdb=" O GLU D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 636 Processing helix chain 'D' and resid 642 through 658 Processing helix chain 'D' and resid 659 through 673 Processing helix chain 'D' and resid 679 through 694 removed outlier: 3.589A pdb=" N SER D 694 " --> pdb=" O ALA D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 720 Processing helix chain 'E' and resid 32 through 39 Processing helix chain 'E' and resid 97 through 102 Processing helix chain 'E' and resid 103 through 107 Processing helix chain 'E' and resid 159 through 169 removed outlier: 3.758A pdb=" N LYS E 163 " --> pdb=" O ALA E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 204 removed outlier: 4.251A pdb=" N SER E 203 " --> pdb=" O GLY E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 259 removed outlier: 3.523A pdb=" N VAL E 259 " --> pdb=" O TYR E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 634 through 652 removed outlier: 3.552A pdb=" N TYR E 652 " --> pdb=" O LEU E 648 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 39 Processing helix chain 'F' and resid 97 through 102 Processing helix chain 'F' and resid 103 through 107 Processing helix chain 'F' and resid 159 through 169 removed outlier: 3.759A pdb=" N LYS F 163 " --> pdb=" O ALA F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 204 removed outlier: 4.252A pdb=" N SER F 203 " --> pdb=" O GLY F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 259 removed outlier: 3.523A pdb=" N VAL F 259 " --> pdb=" O TYR F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 634 through 652 removed outlier: 3.552A pdb=" N TYR F 652 " --> pdb=" O LEU F 648 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 127 through 128 Processing sheet with id=AA2, first strand: chain 'C' and resid 148 through 149 Processing sheet with id=AA3, first strand: chain 'D' and resid 127 through 128 Processing sheet with id=AA4, first strand: chain 'D' and resid 148 through 149 Processing sheet with id=AA5, first strand: chain 'E' and resid 41 through 45 removed outlier: 6.521A pdb=" N GLY E 42 " --> pdb=" O ILE E 244 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N CYS E 246 " --> pdb=" O GLY E 42 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N GLU E 44 " --> pdb=" O CYS E 246 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU E 245 " --> pdb=" O ARG E 74 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL E 63 " --> pdb=" O TYR E 71 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 111 through 115 removed outlier: 5.968A pdb=" N ILE E 128 " --> pdb=" O LEU E 145 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N HIS E 132 " --> pdb=" O GLU E 141 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLU E 141 " --> pdb=" O HIS E 132 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU E 134 " --> pdb=" O LYS E 139 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LYS E 139 " --> pdb=" O GLU E 134 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N THR E 174 " --> pdb=" O GLN E 149 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ALA E 151 " --> pdb=" O SER E 172 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N SER E 172 " --> pdb=" O ALA E 151 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ARG E 223 " --> pdb=" O ILE E 207 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ILE E 207 " --> pdb=" O ARG E 223 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 41 through 45 removed outlier: 6.521A pdb=" N GLY F 42 " --> pdb=" O ILE F 244 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N CYS F 246 " --> pdb=" O GLY F 42 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N GLU F 44 " --> pdb=" O CYS F 246 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU F 245 " --> pdb=" O ARG F 74 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL F 63 " --> pdb=" O TYR F 71 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 111 through 115 removed outlier: 5.967A pdb=" N ILE F 128 " --> pdb=" O LEU F 145 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N HIS F 132 " --> pdb=" O GLU F 141 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLU F 141 " --> pdb=" O HIS F 132 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLU F 134 " --> pdb=" O LYS F 139 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LYS F 139 " --> pdb=" O GLU F 134 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N THR F 174 " --> pdb=" O GLN F 149 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ALA F 151 " --> pdb=" O SER F 172 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N SER F 172 " --> pdb=" O ALA F 151 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ARG F 223 " --> pdb=" O ILE F 207 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ILE F 207 " --> pdb=" O ARG F 223 " (cutoff:3.500A) 1195 hydrogen bonds defined for protein. 3531 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: 3.11 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5636 1.34 - 1.46: 2998 1.46 - 1.58: 9588 1.58 - 1.69: 0 1.69 - 1.81: 202 Bond restraints: 18424 Sorted by residual: bond pdb=" N VAL A 94 " pdb=" CA VAL A 94 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 7.17e+00 bond pdb=" N PHE C 127 " pdb=" CA PHE C 127 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.23e-02 6.61e+03 7.10e+00 bond pdb=" N VAL B 94 " pdb=" CA VAL B 94 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.25e-02 6.40e+03 6.75e+00 bond pdb=" N PHE D 127 " pdb=" CA PHE D 127 " ideal model delta sigma weight residual 1.455 1.487 -0.031 1.21e-02 6.83e+03 6.70e+00 bond pdb=" N PHE D 125 " pdb=" CA PHE D 125 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.29e-02 6.01e+03 6.46e+00 ... (remaining 18419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 24420 1.40 - 2.80: 396 2.80 - 4.21: 63 4.21 - 5.61: 17 5.61 - 7.01: 8 Bond angle restraints: 24904 Sorted by residual: angle pdb=" N HIS F 127 " pdb=" CA HIS F 127 " pdb=" C HIS F 127 " ideal model delta sigma weight residual 107.88 113.44 -5.56 1.41e+00 5.03e-01 1.56e+01 angle pdb=" N HIS E 127 " pdb=" CA HIS E 127 " pdb=" C HIS E 127 " ideal model delta sigma weight residual 107.88 113.42 -5.54 1.41e+00 5.03e-01 1.54e+01 angle pdb=" C GLN B 68 " pdb=" N LEU B 69 " pdb=" CA LEU B 69 " ideal model delta sigma weight residual 121.54 127.82 -6.28 1.91e+00 2.74e-01 1.08e+01 angle pdb=" C GLN A 68 " pdb=" N LEU A 69 " pdb=" CA LEU A 69 " ideal model delta sigma weight residual 121.54 127.80 -6.26 1.91e+00 2.74e-01 1.07e+01 angle pdb=" N THR B 93 " pdb=" CA THR B 93 " pdb=" C THR B 93 " ideal model delta sigma weight residual 111.71 108.19 3.52 1.15e+00 7.56e-01 9.34e+00 ... (remaining 24899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.48: 9999 14.48 - 28.96: 677 28.96 - 43.44: 174 43.44 - 57.91: 44 57.91 - 72.39: 6 Dihedral angle restraints: 10900 sinusoidal: 4358 harmonic: 6542 Sorted by residual: dihedral pdb=" CA LEU B 69 " pdb=" C LEU B 69 " pdb=" N ARG B 70 " pdb=" CA ARG B 70 " ideal model delta harmonic sigma weight residual 180.00 158.05 21.95 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA LEU A 69 " pdb=" C LEU A 69 " pdb=" N ARG A 70 " pdb=" CA ARG A 70 " ideal model delta harmonic sigma weight residual 180.00 158.07 21.93 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA LEU F 48 " pdb=" C LEU F 48 " pdb=" N PRO F 49 " pdb=" CA PRO F 49 " ideal model delta harmonic sigma weight residual 180.00 162.00 18.00 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 10897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1841 0.033 - 0.066: 585 0.066 - 0.099: 126 0.099 - 0.132: 60 0.132 - 0.165: 8 Chirality restraints: 2620 Sorted by residual: chirality pdb=" CA LEU B 90 " pdb=" N LEU B 90 " pdb=" C LEU B 90 " pdb=" CB LEU B 90 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CA CYS C 123 " pdb=" N CYS C 123 " pdb=" C CYS C 123 " pdb=" CB CYS C 123 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.41e-01 chirality pdb=" CA LEU A 90 " pdb=" N LEU A 90 " pdb=" C LEU A 90 " pdb=" CB LEU A 90 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.30e-01 ... (remaining 2617 not shown) Planarity restraints: 3214 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 236 " -0.031 5.00e-02 4.00e+02 4.71e-02 3.54e+00 pdb=" N PRO E 237 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO E 237 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 237 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO F 236 " 0.031 5.00e-02 4.00e+02 4.70e-02 3.54e+00 pdb=" N PRO F 237 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO F 237 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO F 237 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 607 " -0.028 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO C 608 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO C 608 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 608 " -0.024 5.00e-02 4.00e+02 ... (remaining 3211 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1280 2.74 - 3.28: 18448 3.28 - 3.82: 30693 3.82 - 4.36: 33411 4.36 - 4.90: 58803 Nonbonded interactions: 142635 Sorted by model distance: nonbonded pdb=" OE2 GLU D 219 " pdb=" OG SER D 250 " model vdw 2.198 3.040 nonbonded pdb=" OE2 GLU C 219 " pdb=" OG SER C 250 " model vdw 2.198 3.040 nonbonded pdb=" O ARG C 554 " pdb=" OG1 THR C 557 " model vdw 2.227 3.040 nonbonded pdb=" O ARG D 554 " pdb=" OG1 THR D 557 " model vdw 2.228 3.040 nonbonded pdb=" OG SER A 39 " pdb=" OG SER A 42 " model vdw 2.242 3.040 ... (remaining 142630 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.560 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.710 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5937 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 : 0.002 0.033 18438 Z= 0.146 Angle : 0.468 7.010 24932 Z= 0.272 Chirality : 0.037 0.165 2620 Planarity : 0.003 0.047 3214 Dihedral : 10.755 72.392 6702 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.06 % Favored : 94.80 % Rotamer: Outliers : 3.16 % Allowed : 6.05 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.18), residues: 2232 helix: 2.06 (0.13), residues: 1442 sheet: -0.91 (0.39), residues: 162 loop : -1.22 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 70 TYR 0.010 0.001 TYR B 30 PHE 0.013 0.001 PHE B 112 TRP 0.006 0.001 TRP B 118 HIS 0.006 0.001 HIS D 214 Details of bonding type rmsd covalent geometry : bond 0.00242 (18424) covalent geometry : angle 0.46788 (24904) SS BOND : bond 0.00336 ( 14) SS BOND : angle 0.49801 ( 28) hydrogen bonds : bond 0.12324 ( 1195) hydrogen bonds : angle 5.40366 ( 3531) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 380 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.3069 (ptt-90) cc_final: 0.1721 (tmm160) REVERT: A 116 PHE cc_start: 0.7219 (OUTLIER) cc_final: 0.6706 (t80) REVERT: A 176 PHE cc_start: 0.7504 (m-80) cc_final: 0.7259 (m-80) REVERT: A 207 ASN cc_start: 0.8240 (m-40) cc_final: 0.8037 (t0) REVERT: A 216 GLU cc_start: 0.8328 (tm-30) cc_final: 0.8044 (tm-30) REVERT: A 227 TYR cc_start: 0.8310 (OUTLIER) cc_final: 0.7201 (t80) REVERT: A 252 MET cc_start: 0.8169 (mmm) cc_final: 0.7848 (mmm) REVERT: B 176 PHE cc_start: 0.7483 (m-80) cc_final: 0.7164 (m-80) REVERT: B 207 ASN cc_start: 0.8082 (m-40) cc_final: 0.7804 (t0) REVERT: B 227 TYR cc_start: 0.8292 (OUTLIER) cc_final: 0.7468 (t80) REVERT: B 248 MET cc_start: 0.8013 (mtt) cc_final: 0.7652 (mtt) REVERT: B 252 MET cc_start: 0.8305 (mmm) cc_final: 0.8006 (mmm) REVERT: C 216 LYS cc_start: 0.7849 (mttp) cc_final: 0.7501 (tptt) REVERT: C 451 MET cc_start: 0.4313 (tpt) cc_final: 0.4111 (tpt) REVERT: D 216 LYS cc_start: 0.7758 (mttp) cc_final: 0.7346 (tptt) REVERT: D 451 MET cc_start: 0.3708 (tpt) cc_final: 0.3438 (tpt) outliers start: 59 outliers final: 24 residues processed: 414 average time/residue: 0.1502 time to fit residues: 93.3366 Evaluate side-chains 298 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 271 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 227 TYR Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 227 TYR Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain C residue 213 ASN Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 663 MET Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 663 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 216 optimal weight: 20.0000 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 30.0000 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.0970 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 40.0000 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 HIS B 76 HIS ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 GLN C 198 GLN C 271 GLN C 379 HIS C 573 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 595 GLN ** C 670 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 GLN D 271 GLN D 573 GLN ** D 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 595 GLN ** D 670 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 251 GLN E 639 GLN ** E 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 251 GLN F 643 GLN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.247112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 112)---------------| | r_work = 0.4337 r_free = 0.4337 target = 0.187490 restraints weight = 27748.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.182413 restraints weight = 29885.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.185429 restraints weight = 24458.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.185830 restraints weight = 19945.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.186021 restraints weight = 18896.180| |-----------------------------------------------------------------------------| r_work (final): 0.4260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18438 Z= 0.123 Angle : 0.551 8.096 24932 Z= 0.286 Chirality : 0.039 0.213 2620 Planarity : 0.004 0.050 3214 Dihedral : 5.677 56.764 2546 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.11 % Favored : 94.80 % Rotamer: Outliers : 3.10 % Allowed : 10.49 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.18), residues: 2232 helix: 1.95 (0.13), residues: 1470 sheet: -0.53 (0.41), residues: 158 loop : -0.98 (0.27), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 140 TYR 0.014 0.001 TYR D 278 PHE 0.015 0.001 PHE C 647 TRP 0.008 0.001 TRP F 118 HIS 0.010 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00258 (18424) covalent geometry : angle 0.55065 (24904) SS BOND : bond 0.00459 ( 14) SS BOND : angle 0.81040 ( 28) hydrogen bonds : bond 0.03951 ( 1195) hydrogen bonds : angle 4.34659 ( 3531) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 316 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.2932 (ptt-90) cc_final: 0.1596 (tmm160) REVERT: A 76 HIS cc_start: 0.7779 (m90) cc_final: 0.7544 (m90) REVERT: A 116 PHE cc_start: 0.6990 (OUTLIER) cc_final: 0.6612 (t80) REVERT: A 189 PHE cc_start: 0.7636 (OUTLIER) cc_final: 0.7386 (t80) REVERT: A 192 TYR cc_start: 0.8095 (t80) cc_final: 0.7825 (t80) REVERT: A 216 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7607 (tm-30) REVERT: A 227 TYR cc_start: 0.8013 (OUTLIER) cc_final: 0.6879 (t80) REVERT: A 230 PHE cc_start: 0.8491 (t80) cc_final: 0.8151 (t80) REVERT: B 116 PHE cc_start: 0.7005 (OUTLIER) cc_final: 0.6558 (t80) REVERT: B 189 PHE cc_start: 0.7691 (OUTLIER) cc_final: 0.7460 (t80) REVERT: C 216 LYS cc_start: 0.7843 (mttp) cc_final: 0.7052 (tptt) REVERT: C 451 MET cc_start: 0.4148 (tpt) cc_final: 0.3853 (tpt) REVERT: C 532 MET cc_start: 0.6228 (tmm) cc_final: 0.6007 (tmm) REVERT: D 206 LEU cc_start: 0.7115 (mt) cc_final: 0.6847 (mm) REVERT: D 216 LYS cc_start: 0.7741 (mttp) cc_final: 0.6929 (tptt) REVERT: D 440 MET cc_start: 0.2702 (ptp) cc_final: 0.1719 (ppp) REVERT: D 451 MET cc_start: 0.3585 (tpt) cc_final: 0.3213 (tpt) REVERT: D 556 MET cc_start: 0.5664 (mpp) cc_final: 0.5297 (mmt) REVERT: F 84 ARG cc_start: 0.4550 (tpt170) cc_final: 0.4097 (mmm160) outliers start: 58 outliers final: 30 residues processed: 355 average time/residue: 0.1425 time to fit residues: 76.1977 Evaluate side-chains 308 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 273 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 227 TYR Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain C residue 213 ASN Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 515 ILE Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 663 MET Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 319 ASN Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 663 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 102 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 188 optimal weight: 3.9990 chunk 204 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 107 optimal weight: 0.5980 chunk 212 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 185 optimal weight: 5.9990 chunk 198 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 GLN C 254 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 633 HIS D 184 GLN D 198 GLN D 254 GLN D 379 HIS ** D 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 633 HIS ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 643 GLN ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4856 r_free = 0.4856 target = 0.246490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.203682 restraints weight = 27621.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.190366 restraints weight = 39134.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.189332 restraints weight = 34011.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.190561 restraints weight = 28313.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.191034 restraints weight = 21868.398| |-----------------------------------------------------------------------------| r_work (final): 0.4325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18438 Z= 0.148 Angle : 0.567 7.535 24932 Z= 0.297 Chirality : 0.040 0.254 2620 Planarity : 0.004 0.049 3214 Dihedral : 5.557 52.361 2538 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.33 % Favored : 94.58 % Rotamer: Outliers : 2.94 % Allowed : 11.99 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.18), residues: 2232 helix: 1.78 (0.13), residues: 1478 sheet: -0.67 (0.40), residues: 158 loop : -0.96 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 246 TYR 0.019 0.001 TYR C 278 PHE 0.015 0.001 PHE B 112 TRP 0.017 0.001 TRP A 82 HIS 0.009 0.001 HIS D 214 Details of bonding type rmsd covalent geometry : bond 0.00325 (18424) covalent geometry : angle 0.56698 (24904) SS BOND : bond 0.00282 ( 14) SS BOND : angle 0.66186 ( 28) hydrogen bonds : bond 0.03967 ( 1195) hydrogen bonds : angle 4.42669 ( 3531) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 287 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.3053 (ptt-90) cc_final: 0.1687 (tmm160) REVERT: A 29 PHE cc_start: 0.7934 (OUTLIER) cc_final: 0.4348 (t80) REVERT: A 116 PHE cc_start: 0.7006 (OUTLIER) cc_final: 0.6673 (t80) REVERT: A 189 PHE cc_start: 0.7517 (OUTLIER) cc_final: 0.7273 (t80) REVERT: A 216 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7459 (tm-30) REVERT: B 76 HIS cc_start: 0.7481 (m90) cc_final: 0.7202 (m90) REVERT: B 82 TRP cc_start: 0.6831 (m-10) cc_final: 0.6273 (m-10) REVERT: B 116 PHE cc_start: 0.6991 (OUTLIER) cc_final: 0.6585 (t80) REVERT: B 189 PHE cc_start: 0.7559 (OUTLIER) cc_final: 0.7313 (t80) REVERT: C 216 LYS cc_start: 0.7878 (mttp) cc_final: 0.7096 (tptt) REVERT: C 451 MET cc_start: 0.4287 (tpt) cc_final: 0.3982 (tpt) REVERT: C 532 MET cc_start: 0.6348 (tmm) cc_final: 0.6084 (tmm) REVERT: D 212 MET cc_start: 0.5154 (tpt) cc_final: 0.4698 (tpp) REVERT: D 216 LYS cc_start: 0.7793 (mttp) cc_final: 0.7036 (tptt) REVERT: D 440 MET cc_start: 0.2610 (ptp) cc_final: 0.1758 (ppp) REVERT: D 451 MET cc_start: 0.3754 (tpt) cc_final: 0.3337 (tpt) REVERT: E 84 ARG cc_start: 0.4656 (tpt170) cc_final: 0.3863 (mmm160) REVERT: E 189 GLU cc_start: 0.6162 (tp30) cc_final: 0.5939 (tp30) REVERT: F 84 ARG cc_start: 0.4469 (tpt170) cc_final: 0.4115 (mmm160) outliers start: 55 outliers final: 38 residues processed: 325 average time/residue: 0.1380 time to fit residues: 68.0326 Evaluate side-chains 306 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 263 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain C residue 178 GLU Chi-restraints excluded: chain C residue 213 ASN Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 540 GLU Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 663 MET Chi-restraints excluded: chain C residue 694 SER Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 319 ASN Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 663 MET Chi-restraints excluded: chain D residue 694 SER Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain F residue 133 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 164 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 30.0000 chunk 82 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 79 optimal weight: 20.0000 chunk 102 optimal weight: 0.5980 chunk 119 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 GLN ** D 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.243385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.186652 restraints weight = 27672.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.182996 restraints weight = 33882.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.184170 restraints weight = 30165.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.184886 restraints weight = 21872.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.184967 restraints weight = 20297.005| |-----------------------------------------------------------------------------| r_work (final): 0.4270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 18438 Z= 0.156 Angle : 0.583 9.395 24932 Z= 0.304 Chirality : 0.040 0.190 2620 Planarity : 0.004 0.044 3214 Dihedral : 5.566 54.341 2536 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.60 % Favored : 94.31 % Rotamer: Outliers : 3.53 % Allowed : 13.28 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.18), residues: 2232 helix: 1.67 (0.13), residues: 1484 sheet: -0.53 (0.40), residues: 148 loop : -1.01 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 548 TYR 0.028 0.001 TYR D 278 PHE 0.016 0.001 PHE B 112 TRP 0.015 0.001 TRP A 82 HIS 0.009 0.001 HIS D 214 Details of bonding type rmsd covalent geometry : bond 0.00349 (18424) covalent geometry : angle 0.58183 (24904) SS BOND : bond 0.00447 ( 14) SS BOND : angle 1.39006 ( 28) hydrogen bonds : bond 0.03960 ( 1195) hydrogen bonds : angle 4.42452 ( 3531) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 282 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 PHE cc_start: 0.7039 (OUTLIER) cc_final: 0.6675 (t80) REVERT: A 189 PHE cc_start: 0.7593 (OUTLIER) cc_final: 0.7304 (t80) REVERT: A 216 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7538 (tm-30) REVERT: B 116 PHE cc_start: 0.7079 (OUTLIER) cc_final: 0.6621 (t80) REVERT: B 189 PHE cc_start: 0.7583 (OUTLIER) cc_final: 0.7338 (t80) REVERT: B 248 MET cc_start: 0.6964 (mtt) cc_final: 0.6473 (mtt) REVERT: C 212 MET cc_start: 0.5159 (tpt) cc_final: 0.4666 (tpp) REVERT: C 216 LYS cc_start: 0.7906 (mttp) cc_final: 0.7175 (tptt) REVERT: C 451 MET cc_start: 0.4268 (tpt) cc_final: 0.3950 (tpt) REVERT: C 532 MET cc_start: 0.6417 (tmm) cc_final: 0.6078 (tmm) REVERT: D 212 MET cc_start: 0.5224 (tpt) cc_final: 0.4868 (tpp) REVERT: D 216 LYS cc_start: 0.7836 (mttp) cc_final: 0.7030 (tptt) REVERT: D 440 MET cc_start: 0.2579 (ptp) cc_final: 0.1628 (ppp) REVERT: D 451 MET cc_start: 0.3778 (tpt) cc_final: 0.3426 (tpt) REVERT: D 488 MET cc_start: 0.7352 (ppp) cc_final: 0.7051 (ppp) REVERT: E 84 ARG cc_start: 0.4631 (tpt170) cc_final: 0.3943 (mmm160) REVERT: F 84 ARG cc_start: 0.4462 (tpt170) cc_final: 0.4108 (mmm160) outliers start: 66 outliers final: 46 residues processed: 326 average time/residue: 0.1392 time to fit residues: 68.8392 Evaluate side-chains 312 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 262 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 82 TRP Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain C residue 213 ASN Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 515 ILE Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 663 MET Chi-restraints excluded: chain C residue 694 SER Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 319 ASN Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 663 MET Chi-restraints excluded: chain D residue 694 SER Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 211 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 200 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 163 optimal weight: 0.6980 chunk 221 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 152 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 29 optimal weight: 0.0270 chunk 116 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 HIS ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 ASN ** D 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.244310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.190886 restraints weight = 27684.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.190353 restraints weight = 31276.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.189584 restraints weight = 25991.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.189329 restraints weight = 20131.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.189810 restraints weight = 18842.897| |-----------------------------------------------------------------------------| r_work (final): 0.4318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 18438 Z= 0.135 Angle : 0.594 10.950 24932 Z= 0.306 Chirality : 0.040 0.223 2620 Planarity : 0.004 0.042 3214 Dihedral : 5.530 57.118 2536 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.38 % Favored : 94.53 % Rotamer: Outliers : 3.53 % Allowed : 14.78 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.18), residues: 2232 helix: 1.67 (0.13), residues: 1484 sheet: -0.58 (0.41), residues: 128 loop : -0.98 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 246 TYR 0.031 0.001 TYR C 183 PHE 0.015 0.001 PHE B 255 TRP 0.033 0.001 TRP A 82 HIS 0.012 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00301 (18424) covalent geometry : angle 0.59106 (24904) SS BOND : bond 0.00610 ( 14) SS BOND : angle 1.77793 ( 28) hydrogen bonds : bond 0.03859 ( 1195) hydrogen bonds : angle 4.36816 ( 3531) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 283 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 PHE cc_start: 0.7539 (OUTLIER) cc_final: 0.7247 (t80) REVERT: A 216 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7519 (tm-30) REVERT: B 76 HIS cc_start: 0.7351 (m90) cc_final: 0.7021 (m90) REVERT: B 227 TYR cc_start: 0.7839 (m-80) cc_final: 0.7200 (t80) REVERT: C 212 MET cc_start: 0.5059 (tpt) cc_final: 0.4594 (tpp) REVERT: C 216 LYS cc_start: 0.7758 (mttp) cc_final: 0.7159 (tptt) REVERT: C 451 MET cc_start: 0.4255 (tpt) cc_final: 0.3956 (tpt) REVERT: C 532 MET cc_start: 0.6483 (tmm) cc_final: 0.6154 (tmm) REVERT: D 212 MET cc_start: 0.5182 (tpt) cc_final: 0.4786 (tpp) REVERT: D 216 LYS cc_start: 0.7604 (mttp) cc_final: 0.6862 (tptt) REVERT: D 351 MET cc_start: 0.4367 (mmm) cc_final: 0.3717 (mpp) REVERT: D 440 MET cc_start: 0.2598 (ptp) cc_final: 0.1624 (ppp) REVERT: D 451 MET cc_start: 0.3813 (tpt) cc_final: 0.3440 (tpt) REVERT: D 488 MET cc_start: 0.7299 (ppp) cc_final: 0.6968 (ppp) REVERT: E 84 ARG cc_start: 0.4601 (tpt170) cc_final: 0.3943 (mmm160) REVERT: F 84 ARG cc_start: 0.4333 (tpt170) cc_final: 0.4064 (mmm160) REVERT: F 189 GLU cc_start: 0.6024 (tp30) cc_final: 0.5749 (tp30) REVERT: F 641 GLU cc_start: 0.6199 (mm-30) cc_final: 0.5896 (tp30) outliers start: 66 outliers final: 51 residues processed: 326 average time/residue: 0.1318 time to fit residues: 64.7236 Evaluate side-chains 313 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 261 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain C residue 213 ASN Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 515 ILE Chi-restraints excluded: chain C residue 537 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 663 MET Chi-restraints excluded: chain C residue 694 SER Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 319 ASN Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 663 MET Chi-restraints excluded: chain D residue 694 SER Chi-restraints excluded: chain E residue 118 TRP Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 211 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 14 optimal weight: 3.9990 chunk 166 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 176 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 109 optimal weight: 0.6980 chunk 221 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 190 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 ASN ** D 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4851 r_free = 0.4851 target = 0.245925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.194740 restraints weight = 27398.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.190989 restraints weight = 32396.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.181966 restraints weight = 25065.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.182619 restraints weight = 22973.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.183768 restraints weight = 19798.749| |-----------------------------------------------------------------------------| r_work (final): 0.4255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18438 Z= 0.140 Angle : 0.602 10.602 24932 Z= 0.310 Chirality : 0.040 0.286 2620 Planarity : 0.004 0.059 3214 Dihedral : 5.359 59.959 2532 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.56 % Favored : 94.35 % Rotamer: Outliers : 3.48 % Allowed : 14.99 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.18), residues: 2232 helix: 1.62 (0.13), residues: 1486 sheet: -0.69 (0.40), residues: 128 loop : -0.95 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 246 TYR 0.036 0.001 TYR C 278 PHE 0.018 0.001 PHE C 637 TRP 0.027 0.001 TRP A 82 HIS 0.014 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00311 (18424) covalent geometry : angle 0.60014 (24904) SS BOND : bond 0.00389 ( 14) SS BOND : angle 1.39164 ( 28) hydrogen bonds : bond 0.03836 ( 1195) hydrogen bonds : angle 4.39251 ( 3531) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 270 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 HIS cc_start: 0.7227 (m-70) cc_final: 0.6977 (m90) REVERT: A 189 PHE cc_start: 0.7659 (OUTLIER) cc_final: 0.7444 (t80) REVERT: A 216 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7717 (tm-30) REVERT: B 76 HIS cc_start: 0.7582 (m90) cc_final: 0.7195 (m90) REVERT: B 82 TRP cc_start: 0.6673 (m-10) cc_final: 0.6262 (m-10) REVERT: B 227 TYR cc_start: 0.7931 (m-80) cc_final: 0.6772 (t80) REVERT: C 212 MET cc_start: 0.5129 (tpt) cc_final: 0.4617 (tpp) REVERT: C 216 LYS cc_start: 0.7697 (mttp) cc_final: 0.7139 (tptt) REVERT: C 451 MET cc_start: 0.4046 (tpt) cc_final: 0.3730 (tpt) REVERT: C 532 MET cc_start: 0.6489 (tmm) cc_final: 0.6138 (tmm) REVERT: D 212 MET cc_start: 0.5211 (tpt) cc_final: 0.4811 (tpp) REVERT: D 216 LYS cc_start: 0.7578 (mttp) cc_final: 0.6920 (tptt) REVERT: D 351 MET cc_start: 0.4147 (mmm) cc_final: 0.3730 (mpp) REVERT: D 440 MET cc_start: 0.2769 (ptp) cc_final: 0.1611 (ppp) REVERT: D 451 MET cc_start: 0.3626 (tpt) cc_final: 0.3251 (tpt) REVERT: D 556 MET cc_start: 0.5594 (mpp) cc_final: 0.5282 (mmt) REVERT: E 84 ARG cc_start: 0.4765 (tpt170) cc_final: 0.4046 (mmm160) REVERT: E 118 TRP cc_start: 0.3772 (OUTLIER) cc_final: 0.3551 (m-10) REVERT: F 84 ARG cc_start: 0.4526 (tpt170) cc_final: 0.4149 (mmm160) REVERT: F 189 GLU cc_start: 0.6412 (tp30) cc_final: 0.6113 (tp30) REVERT: F 209 ARG cc_start: 0.3923 (tpt170) cc_final: 0.3637 (tpt170) REVERT: F 641 GLU cc_start: 0.6285 (mm-30) cc_final: 0.5976 (tp30) outliers start: 65 outliers final: 53 residues processed: 313 average time/residue: 0.1312 time to fit residues: 62.9336 Evaluate side-chains 309 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 254 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 82 TRP Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain C residue 213 ASN Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 515 ILE Chi-restraints excluded: chain C residue 537 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 663 MET Chi-restraints excluded: chain C residue 694 SER Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 309 SER Chi-restraints excluded: chain D residue 319 ASN Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 663 MET Chi-restraints excluded: chain D residue 694 SER Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 118 TRP Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 211 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 65 optimal weight: 0.9980 chunk 168 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 162 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 203 optimal weight: 30.0000 chunk 68 optimal weight: 0.3980 chunk 36 optimal weight: 0.8980 chunk 32 optimal weight: 0.3980 chunk 16 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4863 r_free = 0.4863 target = 0.247358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.198541 restraints weight = 27569.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.192728 restraints weight = 29702.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.181151 restraints weight = 21194.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.182524 restraints weight = 23638.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.182799 restraints weight = 20121.603| |-----------------------------------------------------------------------------| r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 18438 Z= 0.125 Angle : 0.599 10.883 24932 Z= 0.309 Chirality : 0.040 0.271 2620 Planarity : 0.004 0.085 3214 Dihedral : 5.235 54.589 2532 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.24 % Favored : 94.67 % Rotamer: Outliers : 3.53 % Allowed : 15.52 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.18), residues: 2232 helix: 1.71 (0.13), residues: 1484 sheet: -0.78 (0.39), residues: 128 loop : -0.95 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 548 TYR 0.030 0.001 TYR C 278 PHE 0.019 0.001 PHE B 255 TRP 0.026 0.001 TRP A 82 HIS 0.011 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00274 (18424) covalent geometry : angle 0.59618 (24904) SS BOND : bond 0.00651 ( 14) SS BOND : angle 1.83717 ( 28) hydrogen bonds : bond 0.03712 ( 1195) hydrogen bonds : angle 4.33943 ( 3531) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 273 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LEU cc_start: 0.6008 (OUTLIER) cc_final: 0.5731 (tp) REVERT: A 76 HIS cc_start: 0.7220 (m90) cc_final: 0.6857 (m90) REVERT: A 216 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7826 (tm-30) REVERT: B 69 LEU cc_start: 0.6234 (OUTLIER) cc_final: 0.5977 (tp) REVERT: B 76 HIS cc_start: 0.7622 (m90) cc_final: 0.7130 (m90) REVERT: B 227 TYR cc_start: 0.7916 (m-80) cc_final: 0.7587 (t80) REVERT: C 184 GLN cc_start: 0.7871 (tp-100) cc_final: 0.6999 (tp-100) REVERT: C 188 LYS cc_start: 0.8323 (pttm) cc_final: 0.7994 (pttm) REVERT: C 212 MET cc_start: 0.5092 (tpt) cc_final: 0.4728 (tpp) REVERT: C 216 LYS cc_start: 0.7641 (mttp) cc_final: 0.7001 (tptt) REVERT: C 451 MET cc_start: 0.3888 (tpt) cc_final: 0.3575 (tpt) REVERT: C 532 MET cc_start: 0.6507 (tmm) cc_final: 0.6162 (tmm) REVERT: D 212 MET cc_start: 0.5191 (tpt) cc_final: 0.4798 (tpp) REVERT: D 351 MET cc_start: 0.4049 (mmm) cc_final: 0.3713 (mpp) REVERT: D 440 MET cc_start: 0.2860 (ptp) cc_final: 0.1652 (ppp) REVERT: D 451 MET cc_start: 0.3421 (tpt) cc_final: 0.3064 (tpt) REVERT: D 488 MET cc_start: 0.7920 (ppp) cc_final: 0.7512 (ppp) REVERT: D 532 MET cc_start: 0.6183 (tmm) cc_final: 0.5717 (tmm) REVERT: D 556 MET cc_start: 0.5570 (mpp) cc_final: 0.5363 (mmm) REVERT: E 84 ARG cc_start: 0.4806 (tpt170) cc_final: 0.4091 (mmm160) REVERT: F 84 ARG cc_start: 0.4634 (tpt170) cc_final: 0.4225 (mmm160) REVERT: F 209 ARG cc_start: 0.4157 (tpt170) cc_final: 0.3897 (tpt170) REVERT: F 641 GLU cc_start: 0.6275 (mm-30) cc_final: 0.6023 (tp30) outliers start: 66 outliers final: 53 residues processed: 316 average time/residue: 0.1335 time to fit residues: 65.0168 Evaluate side-chains 305 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 250 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 82 TRP Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 515 ILE Chi-restraints excluded: chain C residue 537 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 663 MET Chi-restraints excluded: chain C residue 694 SER Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 309 SER Chi-restraints excluded: chain D residue 319 ASN Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 663 MET Chi-restraints excluded: chain D residue 694 SER Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 63 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 217 optimal weight: 0.0470 chunk 10 optimal weight: 0.9980 chunk 190 optimal weight: 0.6980 chunk 172 optimal weight: 4.9990 chunk 64 optimal weight: 0.0170 chunk 174 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 199 optimal weight: 0.0070 chunk 44 optimal weight: 0.5980 chunk 183 optimal weight: 8.9990 chunk 55 optimal weight: 50.0000 overall best weight: 0.2734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 ASN ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4879 r_free = 0.4879 target = 0.249266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.198650 restraints weight = 27701.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.195881 restraints weight = 30475.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.188194 restraints weight = 21132.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.187357 restraints weight = 20173.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.188076 restraints weight = 21448.594| |-----------------------------------------------------------------------------| r_work (final): 0.4292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 18438 Z= 0.119 Angle : 0.627 11.220 24932 Z= 0.321 Chirality : 0.040 0.242 2620 Planarity : 0.004 0.043 3214 Dihedral : 4.993 54.013 2530 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.15 % Favored : 94.76 % Rotamer: Outliers : 2.84 % Allowed : 16.92 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.18), residues: 2232 helix: 1.82 (0.13), residues: 1482 sheet: -0.77 (0.40), residues: 132 loop : -0.97 (0.27), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 246 TYR 0.034 0.001 TYR D 278 PHE 0.014 0.001 PHE B 230 TRP 0.030 0.001 TRP A 82 HIS 0.007 0.001 HIS D 214 Details of bonding type rmsd covalent geometry : bond 0.00250 (18424) covalent geometry : angle 0.62542 (24904) SS BOND : bond 0.00504 ( 14) SS BOND : angle 1.60339 ( 28) hydrogen bonds : bond 0.03618 ( 1195) hydrogen bonds : angle 4.29818 ( 3531) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 263 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LEU cc_start: 0.5988 (OUTLIER) cc_final: 0.5694 (tp) REVERT: A 216 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7786 (tm-30) REVERT: B 69 LEU cc_start: 0.6100 (OUTLIER) cc_final: 0.5816 (tp) REVERT: B 76 HIS cc_start: 0.7626 (m90) cc_final: 0.7325 (m-70) REVERT: B 252 MET cc_start: 0.8086 (mpp) cc_final: 0.7740 (mpp) REVERT: C 184 GLN cc_start: 0.7719 (tp40) cc_final: 0.6716 (tp-100) REVERT: C 188 LYS cc_start: 0.8248 (pttm) cc_final: 0.7945 (pttm) REVERT: C 212 MET cc_start: 0.5141 (tpt) cc_final: 0.4754 (tpp) REVERT: C 216 LYS cc_start: 0.7594 (mttp) cc_final: 0.7089 (tptt) REVERT: C 451 MET cc_start: 0.3726 (tpt) cc_final: 0.3430 (tpt) REVERT: C 532 MET cc_start: 0.6554 (tmm) cc_final: 0.6203 (tmm) REVERT: D 212 MET cc_start: 0.5128 (tpt) cc_final: 0.4749 (tpp) REVERT: D 216 LYS cc_start: 0.7029 (mtmm) cc_final: 0.6409 (mmtt) REVERT: D 351 MET cc_start: 0.3930 (mmm) cc_final: 0.3713 (mpp) REVERT: D 440 MET cc_start: 0.2816 (ptp) cc_final: 0.1670 (ppp) REVERT: D 451 MET cc_start: 0.3347 (tpt) cc_final: 0.3012 (tpt) REVERT: D 488 MET cc_start: 0.7804 (ppp) cc_final: 0.7518 (ppp) REVERT: D 532 MET cc_start: 0.6311 (tmm) cc_final: 0.5818 (tmm) REVERT: D 556 MET cc_start: 0.5528 (mpp) cc_final: 0.5297 (mmm) REVERT: D 679 ASP cc_start: 0.5924 (t0) cc_final: 0.5707 (t0) REVERT: E 84 ARG cc_start: 0.4752 (tpt170) cc_final: 0.4072 (mmm160) REVERT: F 84 ARG cc_start: 0.4622 (tpt170) cc_final: 0.4280 (mmm160) outliers start: 53 outliers final: 42 residues processed: 298 average time/residue: 0.1437 time to fit residues: 65.1412 Evaluate side-chains 285 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 241 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 82 TRP Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 537 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 663 MET Chi-restraints excluded: chain C residue 694 SER Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 319 ASN Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 663 MET Chi-restraints excluded: chain D residue 694 SER Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 63 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 139 optimal weight: 9.9990 chunk 119 optimal weight: 0.6980 chunk 191 optimal weight: 9.9990 chunk 168 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 176 optimal weight: 0.6980 chunk 160 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4868 r_free = 0.4868 target = 0.247816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.196435 restraints weight = 27715.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.192264 restraints weight = 30388.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.190105 restraints weight = 24789.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.189230 restraints weight = 21013.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.189034 restraints weight = 21504.168| |-----------------------------------------------------------------------------| r_work (final): 0.4305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 18438 Z= 0.134 Angle : 0.671 16.262 24932 Z= 0.342 Chirality : 0.041 0.195 2620 Planarity : 0.004 0.061 3214 Dihedral : 4.791 53.014 2524 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.51 % Favored : 94.40 % Rotamer: Outliers : 2.84 % Allowed : 16.92 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.18), residues: 2232 helix: 1.66 (0.13), residues: 1488 sheet: -0.86 (0.39), residues: 128 loop : -0.91 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 246 TYR 0.035 0.001 TYR D 278 PHE 0.026 0.001 PHE A 255 TRP 0.026 0.001 TRP A 82 HIS 0.008 0.001 HIS D 214 Details of bonding type rmsd covalent geometry : bond 0.00296 (18424) covalent geometry : angle 0.66906 (24904) SS BOND : bond 0.00463 ( 14) SS BOND : angle 1.47476 ( 28) hydrogen bonds : bond 0.03822 ( 1195) hydrogen bonds : angle 4.33049 ( 3531) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 251 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LEU cc_start: 0.6094 (OUTLIER) cc_final: 0.5788 (tp) REVERT: A 216 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7732 (tm-30) REVERT: A 227 TYR cc_start: 0.7719 (m-80) cc_final: 0.7266 (t80) REVERT: B 69 LEU cc_start: 0.6220 (OUTLIER) cc_final: 0.5947 (tp) REVERT: B 76 HIS cc_start: 0.7600 (m90) cc_final: 0.7283 (m-70) REVERT: B 126 PHE cc_start: 0.7144 (OUTLIER) cc_final: 0.6812 (t80) REVERT: B 227 TYR cc_start: 0.7729 (m-80) cc_final: 0.7371 (t80) REVERT: B 231 MET cc_start: 0.8453 (mpp) cc_final: 0.8026 (mpp) REVERT: C 184 GLN cc_start: 0.7773 (tp40) cc_final: 0.6699 (tp-100) REVERT: C 188 LYS cc_start: 0.8169 (pttm) cc_final: 0.7958 (pttm) REVERT: C 212 MET cc_start: 0.5106 (tpt) cc_final: 0.4644 (tpp) REVERT: C 216 LYS cc_start: 0.7367 (mttp) cc_final: 0.7083 (tptt) REVERT: C 248 GLU cc_start: 0.7521 (tp30) cc_final: 0.7118 (mm-30) REVERT: C 451 MET cc_start: 0.3816 (tpt) cc_final: 0.3522 (tpt) REVERT: C 532 MET cc_start: 0.6591 (tmm) cc_final: 0.6224 (tmm) REVERT: D 212 MET cc_start: 0.5029 (tpt) cc_final: 0.4656 (tpp) REVERT: D 216 LYS cc_start: 0.6948 (mtmm) cc_final: 0.6546 (mmtt) REVERT: D 440 MET cc_start: 0.2859 (ptp) cc_final: 0.1725 (ppp) REVERT: D 451 MET cc_start: 0.3456 (tpt) cc_final: 0.3109 (tpt) REVERT: D 532 MET cc_start: 0.6324 (tmm) cc_final: 0.5814 (tmm) REVERT: D 556 MET cc_start: 0.5590 (mpp) cc_final: 0.5381 (mmm) REVERT: E 84 ARG cc_start: 0.4700 (tpt170) cc_final: 0.4098 (mmm160) REVERT: F 84 ARG cc_start: 0.4589 (tpt170) cc_final: 0.4284 (mmm160) REVERT: F 209 ARG cc_start: 0.3754 (tpt170) cc_final: 0.3460 (tpt170) REVERT: F 641 GLU cc_start: 0.5823 (tp30) cc_final: 0.5616 (tm-30) outliers start: 53 outliers final: 45 residues processed: 288 average time/residue: 0.1482 time to fit residues: 64.3574 Evaluate side-chains 293 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 245 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 82 TRP Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 515 ILE Chi-restraints excluded: chain C residue 537 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 663 MET Chi-restraints excluded: chain C residue 694 SER Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 309 SER Chi-restraints excluded: chain D residue 319 ASN Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 663 MET Chi-restraints excluded: chain D residue 694 SER Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 63 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 197 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 188 optimal weight: 30.0000 chunk 151 optimal weight: 9.9990 chunk 156 optimal weight: 0.7980 chunk 23 optimal weight: 0.0770 chunk 202 optimal weight: 10.0000 chunk 21 optimal weight: 0.0000 chunk 48 optimal weight: 7.9990 chunk 214 optimal weight: 0.9980 chunk 149 optimal weight: 7.9990 overall best weight: 0.5742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 ASN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.248312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.199434 restraints weight = 27664.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.192875 restraints weight = 31262.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.184053 restraints weight = 21640.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.184686 restraints weight = 25933.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.184914 restraints weight = 22590.051| |-----------------------------------------------------------------------------| r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 18438 Z= 0.129 Angle : 0.671 14.282 24932 Z= 0.343 Chirality : 0.041 0.253 2620 Planarity : 0.004 0.059 3214 Dihedral : 4.710 53.260 2522 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.42 % Favored : 94.49 % Rotamer: Outliers : 2.94 % Allowed : 16.86 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.18), residues: 2232 helix: 1.66 (0.13), residues: 1482 sheet: -0.75 (0.40), residues: 132 loop : -0.92 (0.27), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 246 TYR 0.043 0.001 TYR C 183 PHE 0.025 0.001 PHE A 221 TRP 0.031 0.001 TRP A 82 HIS 0.007 0.001 HIS D 214 Details of bonding type rmsd covalent geometry : bond 0.00282 (18424) covalent geometry : angle 0.66930 (24904) SS BOND : bond 0.00439 ( 14) SS BOND : angle 1.43068 ( 28) hydrogen bonds : bond 0.03808 ( 1195) hydrogen bonds : angle 4.31546 ( 3531) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 248 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LEU cc_start: 0.6012 (OUTLIER) cc_final: 0.5463 (tp) REVERT: A 212 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8402 (ttm) REVERT: A 216 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7869 (tm-30) REVERT: A 227 TYR cc_start: 0.7864 (m-80) cc_final: 0.7454 (t80) REVERT: A 252 MET cc_start: 0.8148 (mpp) cc_final: 0.7866 (mpp) REVERT: B 69 LEU cc_start: 0.6103 (OUTLIER) cc_final: 0.5832 (tp) REVERT: B 76 HIS cc_start: 0.7643 (m90) cc_final: 0.7292 (m-70) REVERT: B 212 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8240 (ttm) REVERT: B 227 TYR cc_start: 0.7913 (m-80) cc_final: 0.7691 (t80) REVERT: C 184 GLN cc_start: 0.8045 (tp40) cc_final: 0.6959 (tp-100) REVERT: C 188 LYS cc_start: 0.8275 (pttm) cc_final: 0.8021 (pttm) REVERT: C 212 MET cc_start: 0.5234 (tpt) cc_final: 0.4804 (tpp) REVERT: C 216 LYS cc_start: 0.7286 (mttp) cc_final: 0.6628 (mptt) REVERT: C 248 GLU cc_start: 0.7587 (tp30) cc_final: 0.7137 (mm-30) REVERT: C 451 MET cc_start: 0.3607 (tpt) cc_final: 0.3315 (tpt) REVERT: C 532 MET cc_start: 0.6563 (tmm) cc_final: 0.6246 (tmm) REVERT: D 212 MET cc_start: 0.5149 (tpt) cc_final: 0.4788 (tpp) REVERT: D 216 LYS cc_start: 0.6871 (mtmm) cc_final: 0.6596 (mmtt) REVERT: D 440 MET cc_start: 0.2920 (ptp) cc_final: 0.1726 (ppp) REVERT: D 451 MET cc_start: 0.3223 (tpt) cc_final: 0.2913 (tpt) REVERT: D 532 MET cc_start: 0.6268 (tmm) cc_final: 0.5759 (tmm) REVERT: D 556 MET cc_start: 0.5571 (mpp) cc_final: 0.5332 (mmm) REVERT: E 84 ARG cc_start: 0.4770 (tpt170) cc_final: 0.4106 (mmm160) REVERT: F 84 ARG cc_start: 0.4691 (tpt170) cc_final: 0.4342 (mmm160) REVERT: F 209 ARG cc_start: 0.3924 (tpt170) cc_final: 0.3640 (tpt170) outliers start: 55 outliers final: 46 residues processed: 286 average time/residue: 0.1378 time to fit residues: 60.2337 Evaluate side-chains 295 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 245 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 82 TRP Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 515 ILE Chi-restraints excluded: chain C residue 537 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 663 MET Chi-restraints excluded: chain C residue 694 SER Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 309 SER Chi-restraints excluded: chain D residue 319 ASN Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 663 MET Chi-restraints excluded: chain D residue 694 SER Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 63 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 136 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 179 optimal weight: 7.9990 chunk 140 optimal weight: 9.9990 chunk 134 optimal weight: 5.9990 chunk 116 optimal weight: 40.0000 chunk 128 optimal weight: 0.9990 chunk 180 optimal weight: 7.9990 chunk 101 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 159 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4863 r_free = 0.4863 target = 0.247147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.197363 restraints weight = 27593.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.189919 restraints weight = 32553.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.179823 restraints weight = 25392.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.180759 restraints weight = 28387.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.182512 restraints weight = 23746.046| |-----------------------------------------------------------------------------| r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 18438 Z= 0.140 Angle : 0.676 12.867 24932 Z= 0.345 Chirality : 0.041 0.217 2620 Planarity : 0.004 0.063 3214 Dihedral : 4.731 52.277 2520 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.69 % Favored : 94.22 % Rotamer: Outliers : 2.73 % Allowed : 16.97 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.18), residues: 2232 helix: 1.56 (0.13), residues: 1488 sheet: -0.83 (0.39), residues: 128 loop : -0.88 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 246 TYR 0.043 0.001 TYR C 183 PHE 0.029 0.001 PHE A 255 TRP 0.039 0.001 TRP A 82 HIS 0.009 0.001 HIS D 214 Details of bonding type rmsd covalent geometry : bond 0.00312 (18424) covalent geometry : angle 0.67531 (24904) SS BOND : bond 0.00426 ( 14) SS BOND : angle 1.36625 ( 28) hydrogen bonds : bond 0.03925 ( 1195) hydrogen bonds : angle 4.37737 ( 3531) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4243.32 seconds wall clock time: 73 minutes 33.89 seconds (4413.89 seconds total)