Starting phenix.real_space_refine on Thu Mar 5 16:52:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k5k_22682/03_2026/7k5k_22682.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k5k_22682/03_2026/7k5k_22682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k5k_22682/03_2026/7k5k_22682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k5k_22682/03_2026/7k5k_22682.map" model { file = "/net/cci-nas-00/data/ceres_data/7k5k_22682/03_2026/7k5k_22682.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k5k_22682/03_2026/7k5k_22682.cif" } resolution = 2.66 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= 0.016 sd= 0.156 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mn 12 7.51 5 S 89 5.16 5 C 15486 2.51 5 N 3986 2.21 5 O 4651 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24224 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4020 Classifications: {'peptide': 545} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 17, 'TRANS': 527} Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 180 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 8, 'HIS:plan': 1, 'ASN:plan1': 7, 'GLN:plan1': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 88 Chain: "B" Number of atoms: 4044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4044 Classifications: {'peptide': 545} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 17, 'TRANS': 527} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 5, 'HIS:plan': 1, 'ASN:plan1': 7, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 79 Chain: "C" Number of atoms: 4056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4056 Classifications: {'peptide': 545} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 17, 'TRANS': 527} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 5, 'HIS:plan': 1, 'ASN:plan1': 6, 'PHE:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 69 Chain: "D" Number of atoms: 4036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4036 Classifications: {'peptide': 545} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 17, 'TRANS': 527} Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 5, 'HIS:plan': 1, 'ASN:plan1': 7, 'GLU:plan': 5, 'GLN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "E" Number of atoms: 4009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4009 Classifications: {'peptide': 545} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 17, 'TRANS': 527} Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 8, 'HIS:plan': 1, 'ASN:plan1': 9, 'GLN:plan1': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 94 Chain: "F" Number of atoms: 4023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4023 Classifications: {'peptide': 545} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 17, 'TRANS': 527} Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 6, 'HIS:plan': 1, 'ASN:plan1': 7, 'GLN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 79 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' MN': 2, 'CO3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' MN': 2, 'CO3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' MN': 2, 'CO3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' MN': 2, 'CO3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' MN': 2, 'CO3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' MN': 2, 'CO3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.39, per 1000 atoms: 0.26 Number of scatterers: 24224 At special positions: 0 Unit cell: (145.22, 142.04, 96.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 12 24.99 S 89 16.00 O 4651 8.00 N 3986 7.00 C 15486 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 1.1 seconds 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6012 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 30 sheets defined 36.6% alpha, 17.8% 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 94 through 98 Processing helix chain 'A' and resid 164 through 171 Processing helix chain 'A' and resid 210 through 226 removed outlier: 3.802A pdb=" N LEU A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 258 Processing helix chain 'A' and resid 284 through 288 Processing helix chain 'A' and resid 290 through 311 removed outlier: 4.455A pdb=" N LYS A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 333 removed outlier: 3.570A pdb=" N LYS A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 346 removed outlier: 3.616A pdb=" N GLU A 346 " --> pdb=" O LYS A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 357 removed outlier: 3.567A pdb=" N VAL A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY A 356 " --> pdb=" O TYR A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 415 removed outlier: 4.774A pdb=" N LYS A 413 " --> pdb=" O ASP A 410 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP A 415 " --> pdb=" O MET A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 433 Processing helix chain 'A' and resid 477 through 491 removed outlier: 3.561A pdb=" N THR A 481 " --> pdb=" O GLU A 477 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A 491 " --> pdb=" O VAL A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 509 removed outlier: 3.540A pdb=" N LEU A 508 " --> pdb=" O GLY A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 537 removed outlier: 3.616A pdb=" N THR A 535 " --> pdb=" O SER A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 554 Processing helix chain 'A' and resid 569 through 579 Processing helix chain 'A' and resid 580 through 582 No H-bonds generated for 'chain 'A' and resid 580 through 582' Processing helix chain 'A' and resid 608 through 618 removed outlier: 3.509A pdb=" N ASN A 618 " --> pdb=" O GLU A 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 99 Processing helix chain 'B' and resid 163 through 168 Processing helix chain 'B' and resid 210 through 226 removed outlier: 3.530A pdb=" N THR B 223 " --> pdb=" O TYR B 219 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 258 Processing helix chain 'B' and resid 284 through 288 Processing helix chain 'B' and resid 290 through 311 removed outlier: 4.350A pdb=" N LYS B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 333 Processing helix chain 'B' and resid 340 through 347 removed outlier: 3.678A pdb=" N GLU B 346 " --> pdb=" O LYS B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 357 removed outlier: 3.598A pdb=" N VAL B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY B 356 " --> pdb=" O TYR B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 415 removed outlier: 3.506A pdb=" N MET B 412 " --> pdb=" O ILE B 409 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LYS B 413 " --> pdb=" O ASP B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 433 Processing helix chain 'B' and resid 477 through 491 removed outlier: 3.555A pdb=" N LYS B 491 " --> pdb=" O VAL B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 511 Processing helix chain 'B' and resid 522 through 537 removed outlier: 3.526A pdb=" N THR B 535 " --> pdb=" O SER B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 554 removed outlier: 3.542A pdb=" N ARG B 550 " --> pdb=" O ASN B 547 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER B 551 " --> pdb=" O GLU B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 579 Processing helix chain 'B' and resid 580 through 582 No H-bonds generated for 'chain 'B' and resid 580 through 582' Processing helix chain 'B' and resid 608 through 618 Processing helix chain 'C' and resid 94 through 99 Processing helix chain 'C' and resid 161 through 169 removed outlier: 3.523A pdb=" N GLU C 166 " --> pdb=" O ASN C 162 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE C 167 " --> pdb=" O THR C 163 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS C 169 " --> pdb=" O ASN C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 226 removed outlier: 3.759A pdb=" N LEU C 224 " --> pdb=" O ALA C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 258 Processing helix chain 'C' and resid 284 through 288 Processing helix chain 'C' and resid 290 through 311 removed outlier: 4.486A pdb=" N LYS C 294 " --> pdb=" O GLY C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 332 Processing helix chain 'C' and resid 340 through 347 removed outlier: 3.608A pdb=" N GLU C 346 " --> pdb=" O LYS C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 357 removed outlier: 3.676A pdb=" N VAL C 355 " --> pdb=" O ALA C 351 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY C 356 " --> pdb=" O TYR C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 415 removed outlier: 4.813A pdb=" N LYS C 413 " --> pdb=" O ASP C 410 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP C 415 " --> pdb=" O MET C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 433 Processing helix chain 'C' and resid 477 through 491 removed outlier: 3.504A pdb=" N THR C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS C 491 " --> pdb=" O VAL C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 511 Processing helix chain 'C' and resid 522 through 537 removed outlier: 3.601A pdb=" N THR C 535 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 554 removed outlier: 3.530A pdb=" N ARG C 550 " --> pdb=" O ASN C 547 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N SER C 551 " --> pdb=" O GLU C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 579 Processing helix chain 'C' and resid 580 through 582 No H-bonds generated for 'chain 'C' and resid 580 through 582' Processing helix chain 'C' and resid 608 through 618 Processing helix chain 'D' and resid 165 through 169 Processing helix chain 'D' and resid 210 through 226 removed outlier: 3.697A pdb=" N LEU D 224 " --> pdb=" O ALA D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 258 Processing helix chain 'D' and resid 284 through 288 Processing helix chain 'D' and resid 290 through 311 removed outlier: 4.484A pdb=" N LYS D 294 " --> pdb=" O GLY D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 332 Processing helix chain 'D' and resid 340 through 347 removed outlier: 3.612A pdb=" N GLU D 346 " --> pdb=" O LYS D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 357 removed outlier: 3.675A pdb=" N VAL D 355 " --> pdb=" O ALA D 351 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY D 356 " --> pdb=" O TYR D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 415 removed outlier: 4.819A pdb=" N LYS D 413 " --> pdb=" O ASP D 410 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP D 415 " --> pdb=" O MET D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 433 Processing helix chain 'D' and resid 477 through 491 removed outlier: 3.502A pdb=" N THR D 481 " --> pdb=" O GLU D 477 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS D 491 " --> pdb=" O VAL D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 511 Processing helix chain 'D' and resid 522 through 537 removed outlier: 3.601A pdb=" N THR D 535 " --> pdb=" O SER D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 554 removed outlier: 4.400A pdb=" N SER D 551 " --> pdb=" O GLU D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 579 Processing helix chain 'D' and resid 580 through 582 No H-bonds generated for 'chain 'D' and resid 580 through 582' Processing helix chain 'D' and resid 608 through 618 Processing helix chain 'E' and resid 94 through 99 removed outlier: 4.134A pdb=" N ASP E 98 " --> pdb=" O THR E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 210 through 226 removed outlier: 3.512A pdb=" N THR E 223 " --> pdb=" O TYR E 219 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU E 224 " --> pdb=" O ALA E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 258 Processing helix chain 'E' and resid 284 through 288 Processing helix chain 'E' and resid 290 through 311 removed outlier: 4.281A pdb=" N LYS E 294 " --> pdb=" O GLY E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 333 removed outlier: 3.572A pdb=" N LYS E 331 " --> pdb=" O GLU E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 346 removed outlier: 3.615A pdb=" N GLU E 346 " --> pdb=" O LYS E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 357 removed outlier: 3.567A pdb=" N VAL E 355 " --> pdb=" O ALA E 351 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY E 356 " --> pdb=" O TYR E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 415 removed outlier: 4.801A pdb=" N LYS E 413 " --> pdb=" O ASP E 410 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP E 415 " --> pdb=" O MET E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 433 Processing helix chain 'E' and resid 477 through 491 removed outlier: 3.562A pdb=" N THR E 481 " --> pdb=" O GLU E 477 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS E 491 " --> pdb=" O VAL E 487 " (cutoff:3.500A) Processing helix chain 'E' and resid 504 through 509 removed outlier: 3.545A pdb=" N LEU E 508 " --> pdb=" O GLY E 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 537 removed outlier: 3.622A pdb=" N THR E 535 " --> pdb=" O SER E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 549 through 554 Processing helix chain 'E' and resid 569 through 579 Processing helix chain 'E' and resid 580 through 582 No H-bonds generated for 'chain 'E' and resid 580 through 582' Processing helix chain 'E' and resid 608 through 618 removed outlier: 3.508A pdb=" N ASN E 618 " --> pdb=" O GLU E 614 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 226 removed outlier: 3.538A pdb=" N THR F 223 " --> pdb=" O TYR F 219 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU F 224 " --> pdb=" O ALA F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 258 Processing helix chain 'F' and resid 284 through 288 Processing helix chain 'F' and resid 290 through 311 removed outlier: 4.435A pdb=" N LYS F 294 " --> pdb=" O GLY F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 333 Processing helix chain 'F' and resid 340 through 347 removed outlier: 3.676A pdb=" N GLU F 346 " --> pdb=" O LYS F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 357 removed outlier: 3.588A pdb=" N VAL F 355 " --> pdb=" O ALA F 351 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY F 356 " --> pdb=" O TYR F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 415 removed outlier: 3.509A pdb=" N MET F 412 " --> pdb=" O ILE F 409 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LYS F 413 " --> pdb=" O ASP F 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 433 Processing helix chain 'F' and resid 477 through 491 removed outlier: 3.555A pdb=" N LYS F 491 " --> pdb=" O VAL F 487 " (cutoff:3.500A) Processing helix chain 'F' and resid 504 through 509 removed outlier: 3.641A pdb=" N LEU F 508 " --> pdb=" O GLY F 505 " (cutoff:3.500A) Processing helix chain 'F' and resid 522 through 537 removed outlier: 3.524A pdb=" N THR F 535 " --> pdb=" O SER F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 554 removed outlier: 3.551A pdb=" N ARG F 550 " --> pdb=" O ASN F 547 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N SER F 551 " --> pdb=" O GLU F 548 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 579 Processing helix chain 'F' and resid 580 through 582 No H-bonds generated for 'chain 'F' and resid 580 through 582' Processing helix chain 'F' and resid 608 through 618 Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 105 removed outlier: 6.378A pdb=" N SER A 100 " --> pdb=" O LEU A 278 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LEU A 280 " --> pdb=" O SER A 100 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLU A 102 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ILE A 282 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LYS A 104 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL A 233 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N HIS A 281 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE A 235 " --> pdb=" O HIS A 281 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE A 118 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL A 201 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N PHE A 120 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N CYS A 203 " --> pdb=" O PHE A 120 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N LEU A 122 " --> pdb=" O CYS A 203 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 338 through 339 removed outlier: 4.344A pdb=" N ILE A 392 " --> pdb=" O CYS A 446 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASN A 448 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE A 394 " --> pdb=" O ASN A 448 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 338 through 339 removed outlier: 4.269A pdb=" N ALA A 444 " --> pdb=" O GLY A 389 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LYS A 384 " --> pdb=" O TYR A 496 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N VAL A 498 " --> pdb=" O LYS A 384 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ALA A 386 " --> pdb=" O VAL A 498 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ILE A 500 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE A 388 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE A 497 " --> pdb=" O ALA A 588 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ILE A 590 " --> pdb=" O ILE A 497 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ASP A 499 " --> pdb=" O ILE A 590 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY A 517 " --> pdb=" O ASP A 591 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ALA A 516 " --> pdb=" O TRP A 541 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 460 through 462 Processing sheet with id=AA5, first strand: chain 'A' and resid 597 through 598 Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.437A pdb=" N SER B 100 " --> pdb=" O LEU B 278 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LEU B 280 " --> pdb=" O SER B 100 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLU B 102 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ILE B 282 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LYS B 104 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE B 118 " --> pdb=" O ALA B 199 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N VAL B 201 " --> pdb=" O ILE B 118 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N PHE B 120 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TYR B 200 " --> pdb=" O SER B 183 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N SER B 183 " --> pdb=" O TYR B 200 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 338 through 339 removed outlier: 4.335A pdb=" N ILE B 392 " --> pdb=" O CYS B 446 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASN B 448 " --> pdb=" O ILE B 392 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N PHE B 394 " --> pdb=" O ASN B 448 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 338 through 339 removed outlier: 4.230A pdb=" N ALA B 444 " --> pdb=" O GLY B 389 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LYS B 384 " --> pdb=" O TYR B 496 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N VAL B 498 " --> pdb=" O LYS B 384 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ALA B 386 " --> pdb=" O VAL B 498 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE B 500 " --> pdb=" O ALA B 386 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE B 388 " --> pdb=" O ILE B 500 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE B 497 " --> pdb=" O ALA B 588 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ILE B 590 " --> pdb=" O ILE B 497 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ASP B 499 " --> pdb=" O ILE B 590 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ALA B 516 " --> pdb=" O TRP B 541 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 460 through 462 Processing sheet with id=AB1, first strand: chain 'B' and resid 597 through 598 Processing sheet with id=AB2, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.521A pdb=" N SER C 100 " --> pdb=" O LEU C 278 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N LEU C 280 " --> pdb=" O SER C 100 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLU C 102 " --> pdb=" O LEU C 280 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ILE C 282 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N LYS C 104 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL C 233 " --> pdb=" O SER C 279 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N HIS C 281 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE C 235 " --> pdb=" O HIS C 281 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE C 118 " --> pdb=" O ALA C 199 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N VAL C 201 " --> pdb=" O ILE C 118 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE C 120 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N TYR C 200 " --> pdb=" O SER C 183 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER C 183 " --> pdb=" O TYR C 200 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 338 through 339 removed outlier: 4.318A pdb=" N ILE C 392 " --> pdb=" O CYS C 446 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ASN C 448 " --> pdb=" O ILE C 392 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N PHE C 394 " --> pdb=" O ASN C 448 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 338 through 339 removed outlier: 4.255A pdb=" N ALA C 444 " --> pdb=" O GLY C 389 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR C 496 " --> pdb=" O LYS C 384 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY C 517 " --> pdb=" O ASP C 591 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ALA C 516 " --> pdb=" O TRP C 541 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 460 through 462 Processing sheet with id=AB6, first strand: chain 'C' and resid 597 through 598 Processing sheet with id=AB7, first strand: chain 'D' and resid 100 through 105 removed outlier: 6.554A pdb=" N SER D 100 " --> pdb=" O LEU D 278 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N LEU D 280 " --> pdb=" O SER D 100 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLU D 102 " --> pdb=" O LEU D 280 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ILE D 282 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LYS D 104 " --> pdb=" O ILE D 282 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL D 233 " --> pdb=" O SER D 279 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N HIS D 281 " --> pdb=" O VAL D 233 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE D 235 " --> pdb=" O HIS D 281 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE D 118 " --> pdb=" O ALA D 199 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL D 201 " --> pdb=" O ILE D 118 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N PHE D 120 " --> pdb=" O VAL D 201 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU D 198 " --> pdb=" O SER D 185 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N SER D 185 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N TYR D 200 " --> pdb=" O SER D 183 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER D 183 " --> pdb=" O TYR D 200 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 338 through 339 removed outlier: 4.319A pdb=" N ILE D 392 " --> pdb=" O CYS D 446 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ASN D 448 " --> pdb=" O ILE D 392 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE D 394 " --> pdb=" O ASN D 448 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 338 through 339 removed outlier: 4.256A pdb=" N ALA D 444 " --> pdb=" O GLY D 389 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LYS D 384 " --> pdb=" O TYR D 496 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N VAL D 498 " --> pdb=" O LYS D 384 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ALA D 386 " --> pdb=" O VAL D 498 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE D 500 " --> pdb=" O ALA D 386 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE D 388 " --> pdb=" O ILE D 500 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE D 497 " --> pdb=" O ALA D 588 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ILE D 590 " --> pdb=" O ILE D 497 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASP D 499 " --> pdb=" O ILE D 590 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY D 517 " --> pdb=" O ASP D 591 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ALA D 516 " --> pdb=" O TRP D 541 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 460 through 462 Processing sheet with id=AC2, first strand: chain 'D' and resid 597 through 598 Processing sheet with id=AC3, first strand: chain 'E' and resid 100 through 105 removed outlier: 6.365A pdb=" N SER E 100 " --> pdb=" O LEU E 278 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LEU E 280 " --> pdb=" O SER E 100 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLU E 102 " --> pdb=" O LEU E 280 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE E 282 " --> pdb=" O GLU E 102 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LYS E 104 " --> pdb=" O ILE E 282 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL E 233 " --> pdb=" O SER E 279 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N HIS E 281 " --> pdb=" O VAL E 233 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE E 235 " --> pdb=" O HIS E 281 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE E 118 " --> pdb=" O ALA E 199 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N VAL E 201 " --> pdb=" O ILE E 118 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N PHE E 120 " --> pdb=" O VAL E 201 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N CYS E 203 " --> pdb=" O PHE E 120 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LEU E 122 " --> pdb=" O CYS E 203 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N LEU E 198 " --> pdb=" O SER E 185 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N SER E 185 " --> pdb=" O LEU E 198 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TYR E 200 " --> pdb=" O SER E 183 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER E 183 " --> pdb=" O TYR E 200 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 338 through 339 removed outlier: 4.345A pdb=" N ILE E 392 " --> pdb=" O CYS E 446 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ASN E 448 " --> pdb=" O ILE E 392 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N PHE E 394 " --> pdb=" O ASN E 448 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 338 through 339 removed outlier: 4.269A pdb=" N ALA E 444 " --> pdb=" O GLY E 389 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LYS E 384 " --> pdb=" O TYR E 496 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N VAL E 498 " --> pdb=" O LYS E 384 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ALA E 386 " --> pdb=" O VAL E 498 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE E 500 " --> pdb=" O ALA E 386 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE E 388 " --> pdb=" O ILE E 500 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE E 497 " --> pdb=" O ALA E 588 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ILE E 590 " --> pdb=" O ILE E 497 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASP E 499 " --> pdb=" O ILE E 590 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY E 517 " --> pdb=" O ASP E 591 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ALA E 516 " --> pdb=" O TRP E 541 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 460 through 462 Processing sheet with id=AC7, first strand: chain 'E' and resid 597 through 598 Processing sheet with id=AC8, first strand: chain 'F' and resid 100 through 105 removed outlier: 6.432A pdb=" N SER F 100 " --> pdb=" O LEU F 278 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEU F 280 " --> pdb=" O SER F 100 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLU F 102 " --> pdb=" O LEU F 280 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ILE F 282 " --> pdb=" O GLU F 102 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LYS F 104 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N TYR F 200 " --> pdb=" O ILE F 118 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N PHE F 120 " --> pdb=" O TYR F 200 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N GLY F 202 " --> pdb=" O PHE F 120 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU F 122 " --> pdb=" O GLY F 202 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY F 204 " --> pdb=" O LEU F 122 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N TYR F 200 " --> pdb=" O SER F 183 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N SER F 183 " --> pdb=" O TYR F 200 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 338 through 339 removed outlier: 4.332A pdb=" N ILE F 392 " --> pdb=" O CYS F 446 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASN F 448 " --> pdb=" O ILE F 392 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N PHE F 394 " --> pdb=" O ASN F 448 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 338 through 339 removed outlier: 4.264A pdb=" N ALA F 444 " --> pdb=" O GLY F 389 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LYS F 384 " --> pdb=" O TYR F 496 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N VAL F 498 " --> pdb=" O LYS F 384 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ALA F 386 " --> pdb=" O VAL F 498 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ILE F 500 " --> pdb=" O ALA F 386 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE F 388 " --> pdb=" O ILE F 500 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE F 497 " --> pdb=" O ALA F 588 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ILE F 590 " --> pdb=" O ILE F 497 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASP F 499 " --> pdb=" O ILE F 590 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ALA F 516 " --> pdb=" O TRP F 541 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 460 through 462 Processing sheet with id=AD3, first strand: chain 'F' and resid 597 through 598 993 hydrogen bonds defined for protein. 2673 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: 4.81 Time building geometry restraints manager: 2.76 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: 7811 1.34 - 1.46: 4015 1.46 - 1.57: 12717 1.57 - 1.69: 0 1.69 - 1.81: 131 Bond restraints: 24674 Sorted by residual: bond pdb=" CA GLY C 181 " pdb=" C GLY C 181 " ideal model delta sigma weight residual 1.530 1.510 0.020 1.04e-02 9.25e+03 3.76e+00 bond pdb=" N GLY C 181 " pdb=" CA GLY C 181 " ideal model delta sigma weight residual 1.464 1.444 0.021 1.12e-02 7.97e+03 3.38e+00 bond pdb=" C LEU A 83 " pdb=" N ASP A 84 " ideal model delta sigma weight residual 1.331 1.292 0.039 2.83e-02 1.25e+03 1.89e+00 bond pdb=" C CYS A 111 " pdb=" N PRO A 112 " ideal model delta sigma weight residual 1.335 1.351 -0.017 1.28e-02 6.10e+03 1.72e+00 bond pdb=" CG1 ILE A 529 " pdb=" CD1 ILE A 529 " ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.57e+00 ... (remaining 24669 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 31944 1.45 - 2.89: 1278 2.89 - 4.34: 228 4.34 - 5.79: 33 5.79 - 7.24: 17 Bond angle restraints: 33500 Sorted by residual: angle pdb=" CA TYR C 300 " pdb=" CB TYR C 300 " pdb=" CG TYR C 300 " ideal model delta sigma weight residual 113.90 107.04 6.86 1.80e+00 3.09e-01 1.45e+01 angle pdb=" CA TYR D 300 " pdb=" CB TYR D 300 " pdb=" CG TYR D 300 " ideal model delta sigma weight residual 113.90 107.07 6.83 1.80e+00 3.09e-01 1.44e+01 angle pdb=" C THR C 87 " pdb=" N ILE C 88 " pdb=" CA ILE C 88 " ideal model delta sigma weight residual 122.59 119.98 2.61 7.20e-01 1.93e+00 1.32e+01 angle pdb=" C TYR A 187 " pdb=" CA TYR A 187 " pdb=" CB TYR A 187 " ideal model delta sigma weight residual 111.74 106.80 4.94 1.37e+00 5.33e-01 1.30e+01 angle pdb=" CA TYR A 300 " pdb=" CB TYR A 300 " pdb=" CG TYR A 300 " ideal model delta sigma weight residual 113.90 107.56 6.34 1.80e+00 3.09e-01 1.24e+01 ... (remaining 33495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 13105 17.67 - 35.33: 1150 35.33 - 53.00: 271 53.00 - 70.66: 76 70.66 - 88.33: 22 Dihedral angle restraints: 14624 sinusoidal: 5198 harmonic: 9426 Sorted by residual: dihedral pdb=" CA ASP A 161 " pdb=" C ASP A 161 " pdb=" N ASN A 162 " pdb=" CA ASN A 162 " ideal model delta harmonic sigma weight residual 180.00 -143.16 -36.84 0 5.00e+00 4.00e-02 5.43e+01 dihedral pdb=" CA PRO F 126 " pdb=" C PRO F 126 " pdb=" N LYS F 127 " pdb=" CA LYS F 127 " ideal model delta harmonic sigma weight residual -180.00 -149.66 -30.34 0 5.00e+00 4.00e-02 3.68e+01 dihedral pdb=" CA CYS F 111 " pdb=" C CYS F 111 " pdb=" N PRO F 112 " pdb=" CA PRO F 112 " ideal model delta harmonic sigma weight residual 180.00 -150.61 -29.39 0 5.00e+00 4.00e-02 3.46e+01 ... (remaining 14621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1934 0.033 - 0.066: 1326 0.066 - 0.099: 440 0.099 - 0.132: 156 0.132 - 0.165: 22 Chirality restraints: 3878 Sorted by residual: chirality pdb=" CB ILE B 500 " pdb=" CA ILE B 500 " pdb=" CG1 ILE B 500 " pdb=" CG2 ILE B 500 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.77e-01 chirality pdb=" CB ILE F 500 " pdb=" CA ILE F 500 " pdb=" CG1 ILE F 500 " pdb=" CG2 ILE F 500 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.63e-01 chirality pdb=" CB ILE C 500 " pdb=" CA ILE C 500 " pdb=" CG1 ILE C 500 " pdb=" CG2 ILE C 500 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.62e-01 ... (remaining 3875 not shown) Planarity restraints: 4288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 300 " 0.025 2.00e-02 2.50e+03 1.55e-02 4.78e+00 pdb=" CG TYR D 300 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR D 300 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR D 300 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR D 300 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR D 300 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR D 300 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR D 300 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 317 " -0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO C 318 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 318 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 318 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 300 " -0.024 2.00e-02 2.50e+03 1.52e-02 4.65e+00 pdb=" CG TYR C 300 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR C 300 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR C 300 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR C 300 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 300 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR C 300 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 300 " -0.004 2.00e-02 2.50e+03 ... (remaining 4285 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 72 2.36 - 2.99: 12702 2.99 - 3.63: 35230 3.63 - 4.26: 60048 4.26 - 4.90: 98110 Nonbonded interactions: 206162 Sorted by model distance: nonbonded pdb=" O ASP E 475 " pdb="MN MN E 702 " model vdw 1.722 2.320 nonbonded pdb=" O ASP A 475 " pdb="MN MN A 702 " model vdw 1.722 2.320 nonbonded pdb=" O ASP C 475 " pdb="MN MN C 703 " model vdw 1.750 2.320 nonbonded pdb=" O ASP D 475 " pdb="MN MN D 703 " model vdw 1.752 2.320 nonbonded pdb=" NZ LYS A 390 " pdb="MN MN A 703 " model vdw 1.806 2.400 ... (remaining 206157 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 75 through 81 or (resid 82 and (name N or name CA or name \ C or name O or name CB )) or resid 83 through 97 or (resid 98 and (name N or nam \ e CA or name C or name O or name CB )) or resid 99 or (resid 100 and (name N or \ name CA or name C or name O or name CB )) or resid 101 or (resid 102 and (name N \ or name CA or name C or name O or name CB )) or resid 103 through 110 or (resid \ 111 and (name N or name CA or name C or name O or name CB )) or resid 112 throu \ gh 113 or (resid 114 through 115 and (name N or name CA or name C or name O or n \ ame CB )) or resid 116 through 178 or (resid 179 and (name N or name CA or name \ C or name O or name CB )) or resid 180 through 182 or (resid 183 and (name N or \ name CA or name C or name O or name CB )) or resid 184 through 189 or (resid 190 \ and (name N or name CA or name C or name O or name CB )) or resid 191 through 1 \ 93 or (resid 194 and (name N or name CA or name C or name O or name CB )) or res \ id 195 through 210 or (resid 211 and (name N or name CA or name C or name O or n \ ame CB )) or resid 212 through 269 or (resid 270 through 272 and (name N or name \ CA or name C or name O or name CB )) or resid 273 through 379 or (resid 380 and \ (name N or name CA or name C or name O or name CB )) or resid 381 through 498 o \ r (resid 499 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 00 through 509 or (resid 510 and (name N or name CA or name C or name O or name \ CB )) or resid 511 through 523 or (resid 524 and (name N or name CA or name C or \ name O or name CB )) or resid 525 through 564 or (resid 565 and (name N or name \ CA or name C or name O or name CB )) or resid 566 through 599 or (resid 600 thr \ ough 601 and (name N or name CA or name C or name O or name CB )) or resid 602 t \ hrough 618 or (resid 619 and (name N or name CA or name C or name O or name CB ) \ ) or resid 701 through 703)) selection = (chain 'B' and (resid 75 through 81 or (resid 82 and (name N or name CA or name \ C or name O or name CB )) or resid 83 through 97 or (resid 98 and (name N or nam \ e CA or name C or name O or name CB )) or resid 99 or (resid 100 and (name N or \ name CA or name C or name O or name CB )) or resid 101 through 104 or (resid 105 \ and (name N or name CA or name C or name O or name CB )) or resid 106 through 1 \ 10 or (resid 111 and (name N or name CA or name C or name O or name CB )) or res \ id 112 through 126 or (resid 127 through 131 and (name N or name CA or name C or \ name O or name CB )) or (resid 132 through 170 and (name N or name CA or name C \ or name O or name CB )) or resid 171 through 178 or (resid 179 and (name N or n \ ame CA or name C or name O or name CB )) or resid 180 through 182 or (resid 183 \ and (name N or name CA or name C or name O or name CB )) or resid 184 through 18 \ 9 or (resid 190 and (name N or name CA or name C or name O or name CB )) or resi \ d 191 through 193 or (resid 194 and (name N or name CA or name C or name O or na \ me CB )) or resid 195 through 228 or (resid 229 and (name N or name CA or name C \ or name O or name CB )) or resid 230 or (resid 231 and (name N or name CA or na \ me C or name O or name CB )) or resid 232 through 239 or (resid 240 and (name N \ or name CA or name C or name O or name CB )) or resid 241 through 270 or (resid \ 271 through 272 and (name N or name CA or name C or name O or name CB )) or resi \ d 273 through 373 or (resid 374 and (name N or name CA or name C or name O or na \ me CB )) or resid 375 through 377 or (resid 378 through 380 and (name N or name \ CA or name C or name O or name CB )) or resid 381 through 523 or (resid 524 and \ (name N or name CA or name C or name O or name CB )) or resid 525 through 582 or \ (resid 583 and (name N or name CA or name C or name O or name CB )) or resid 58 \ 4 through 599 or (resid 600 through 601 and (name N or name CA or name C or name \ O or name CB )) or resid 602 through 618 or (resid 619 and (name N or name CA o \ r name C or name O or name CB )) or resid 701 through 703)) selection = (chain 'C' and (resid 75 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O or name CB )) or resid 103 through 113 or (resid 114 through 115 a \ nd (name N or name CA or name C or name O or name CB )) or resid 116 through 151 \ or (resid 152 through 170 and (name N or name CA or name C or name O or name CB \ )) or resid 171 through 178 or (resid 179 and (name N or name CA or name C or n \ ame O or name CB )) or resid 180 through 182 or (resid 183 and (name N or name C \ A or name C or name O or name CB )) or resid 184 through 189 or (resid 190 and ( \ name N or name CA or name C or name O or name CB )) or resid 191 through 193 or \ (resid 194 and (name N or name CA or name C or name O or name CB )) or resid 195 \ through 239 or (resid 240 and (name N or name CA or name C or name O or name CB \ )) or resid 241 through 266 or (resid 267 and (name N or name CA or name C or n \ ame O or name CB )) or resid 268 through 269 or (resid 270 through 272 and (name \ N or name CA or name C or name O or name CB )) or resid 273 through 377 or (res \ id 378 through 380 and (name N or name CA or name C or name O or name CB )) or r \ esid 381 through 498 or (resid 499 and (name N or name CA or name C or name O or \ name CB )) or resid 500 through 509 or (resid 510 and (name N or name CA or nam \ e C or name O or name CB )) or resid 511 through 564 or (resid 565 and (name N o \ r name CA or name C or name O or name CB )) or resid 566 through 582 or (resid 5 \ 83 and (name N or name CA or name C or name O or name CB )) or resid 584 through \ 599 or (resid 600 through 601 and (name N or name CA or name C or name O or nam \ e CB )) or resid 602 through 618 or (resid 619 and (name N or name CA or name C \ or name O or name CB )) or resid 701 through 703)) selection = (chain 'D' and (resid 75 through 81 or (resid 82 and (name N or name CA or name \ C or name O or name CB )) or resid 83 through 97 or (resid 98 and (name N or nam \ e CA or name C or name O or name CB )) or resid 99 or (resid 100 and (name N or \ name CA or name C or name O or name CB )) or resid 101 or (resid 102 and (name N \ or name CA or name C or name O or name CB )) or resid 103 through 108 or (resid \ 109 through 111 and (name N or name CA or name C or name O or name CB )) or res \ id 112 through 113 or (resid 114 through 115 and (name N or name CA or name C or \ name O or name CB )) or resid 116 through 152 or (resid 153 through 170 and (na \ me N or name CA or name C or name O or name CB )) or resid 171 through 178 or (r \ esid 179 and (name N or name CA or name C or name O or name CB )) or resid 180 t \ hrough 189 or (resid 190 and (name N or name CA or name C or name O or name CB ) \ ) or resid 191 through 193 or (resid 194 and (name N or name CA or name C or nam \ e O or name CB )) or resid 195 through 239 or (resid 240 and (name N or name CA \ or name C or name O or name CB )) or resid 241 through 266 or (resid 267 and (na \ me N or name CA or name C or name O or name CB )) or resid 268 through 269 or (r \ esid 270 through 272 and (name N or name CA or name C or name O or name CB )) or \ resid 273 through 373 or (resid 374 and (name N or name CA or name C or name O \ or name CB )) or resid 375 through 377 or (resid 378 through 380 and (name N or \ name CA or name C or name O or name CB )) or resid 381 through 509 or (resid 510 \ and (name N or name CA or name C or name O or name CB )) or resid 511 through 5 \ 64 or (resid 565 and (name N or name CA or name C or name O or name CB )) or res \ id 566 through 582 or (resid 583 and (name N or name CA or name C or name O or n \ ame CB )) or resid 584 through 703)) selection = (chain 'E' and (resid 75 through 97 or (resid 98 and (name N or name CA or name \ C or name O or name CB )) or resid 99 or (resid 100 and (name N or name CA or na \ me C or name O or name CB )) or resid 101 or (resid 102 and (name N or name CA o \ r name C or name O or name CB )) or resid 103 through 110 or (resid 111 and (nam \ e N or name CA or name C or name O or name CB )) or resid 112 through 113 or (re \ sid 114 through 115 and (name N or name CA or name C or name O or name CB )) or \ resid 116 through 128 or (resid 129 through 131 and (name N or name CA or name C \ or name O or name CB )) or resid 132 through 178 or (resid 179 and (name N or n \ ame CA or name C or name O or name CB )) or resid 180 through 182 or (resid 183 \ and (name N or name CA or name C or name O or name CB )) or resid 184 through 19 \ 3 or (resid 194 and (name N or name CA or name C or name O or name CB )) or resi \ d 195 through 210 or (resid 211 and (name N or name CA or name C or name O or na \ me CB )) or resid 212 through 266 or (resid 267 and (name N or name CA or name C \ or name O or name CB )) or resid 268 through 269 or (resid 270 through 272 and \ (name N or name CA or name C or name O or name CB )) or resid 273 through 373 or \ (resid 374 and (name N or name CA or name C or name O or name CB )) or resid 37 \ 5 through 377 or (resid 378 through 380 and (name N or name CA or name C or name \ O or name CB )) or resid 381 through 509 or (resid 510 and (name N or name CA o \ r name C or name O or name CB )) or resid 511 through 564 or (resid 565 and (nam \ e N or name CA or name C or name O or name CB )) or resid 566 through 618 or (re \ sid 619 and (name N or name CA or name C or name O or name CB )) or resid 701 th \ rough 703)) selection = (chain 'F' and (resid 75 through 81 or (resid 82 and (name N or name CA or name \ C or name O or name CB )) or resid 83 through 97 or (resid 98 and (name N or nam \ e CA or name C or name O or name CB )) or resid 99 or (resid 100 and (name N or \ name CA or name C or name O or name CB )) or resid 101 or (resid 102 and (name N \ or name CA or name C or name O or name CB )) or resid 103 through 110 or (resid \ 111 and (name N or name CA or name C or name O or name CB )) or resid 112 throu \ gh 113 or (resid 114 through 115 and (name N or name CA or name C or name O or n \ ame CB )) or resid 116 through 182 or (resid 183 and (name N or name CA or name \ C or name O or name CB )) or resid 184 through 189 or (resid 190 and (name N or \ name CA or name C or name O or name CB )) or resid 191 through 210 or (resid 211 \ and (name N or name CA or name C or name O or name CB )) or resid 212 through 2 \ 30 or (resid 231 and (name N or name CA or name C or name O or name CB )) or res \ id 232 through 270 or (resid 271 through 272 and (name N or name CA or name C or \ name O or name CB )) or resid 273 through 373 or (resid 374 and (name N or name \ CA or name C or name O or name CB )) or resid 375 through 377 or (resid 378 thr \ ough 380 and (name N or name CA or name C or name O or name CB )) or resid 381 t \ hrough 509 or (resid 510 and (name N or name CA or name C or name O or name CB ) \ ) or resid 511 through 599 or (resid 600 through 601 and (name N or name CA or n \ ame C or name O or name CB )) or resid 602 through 618 or (resid 619 and (name N \ or name CA or name C or name O or name CB )) or resid 701 through 703)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.640 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 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:9.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 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 : 0.007 0.049 24674 Z= 0.299 Angle : 0.693 7.235 33500 Z= 0.387 Chirality : 0.048 0.165 3878 Planarity : 0.004 0.054 4288 Dihedral : 15.266 88.326 8612 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.22 % Favored : 89.75 % Rotamer: Outliers : 4.06 % Allowed : 15.54 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 are not related in a simple way. whole: -3.21 (0.12), residues: 3258 helix: -1.64 (0.13), residues: 1054 sheet: -1.33 (0.19), residues: 606 loop : -2.82 (0.12), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 610 TYR 0.035 0.003 TYR D 300 PHE 0.020 0.003 PHE C 299 TRP 0.008 0.002 TRP D 587 HIS 0.006 0.001 HIS A 252 Details of bonding type rmsd covalent geometry : bond 0.00704 (24674) covalent geometry : angle 0.69271 (33500) hydrogen bonds : bond 0.18788 ( 933) hydrogen bonds : angle 7.13671 ( 2673) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 232 time to evaluate : 0.811 Fit side-chains REVERT: A 275 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8570 (mm) REVERT: B 122 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8343 (mt) REVERT: B 193 LYS cc_start: 0.4833 (OUTLIER) cc_final: 0.4558 (tmmt) REVERT: B 414 PHE cc_start: 0.9038 (OUTLIER) cc_final: 0.8102 (p90) REVERT: C 115 GLU cc_start: 0.5202 (OUTLIER) cc_final: 0.4577 (mm-30) REVERT: C 153 ILE cc_start: 0.7902 (OUTLIER) cc_final: 0.7636 (mt) REVERT: C 619 ASP cc_start: 0.7130 (OUTLIER) cc_final: 0.6878 (m-30) REVERT: E 384 LYS cc_start: 0.8227 (mtpp) cc_final: 0.7992 (mttt) REVERT: F 275 ILE cc_start: 0.8669 (mt) cc_final: 0.8461 (mt) REVERT: F 384 LYS cc_start: 0.8268 (mtpp) cc_final: 0.7964 (mttt) REVERT: F 568 LYS cc_start: 0.8519 (mttt) cc_final: 0.8291 (mttp) outliers start: 99 outliers final: 64 residues processed: 320 average time/residue: 0.5631 time to fit residues: 209.6142 Evaluate side-chains 270 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 199 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 414 PHE Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 455 TYR Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 619 ASP Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 190 ASN Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 455 TYR Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 561 ASN Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 111 CYS Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain E residue 510 SER Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 111 CYS Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 455 TYR Chi-restraints excluded: chain F residue 464 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.0000 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN A 230 HIS A 281 HIS A 307 GLN A 363 ASN A 436 ASN A 473 ASN A 527 ASN B 230 HIS B 307 GLN B 363 ASN B 436 ASN B 527 ASN B 584 ASN C 79 GLN C 230 HIS C 307 GLN C 363 ASN C 473 ASN C 527 ASN D 230 HIS D 307 GLN D 363 ASN D 380 ASN D 436 ASN D 473 ASN D 527 ASN E 230 HIS E 307 GLN E 363 ASN E 473 ASN E 527 ASN F 230 HIS F 307 GLN F 363 ASN F 527 ASN F 584 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.141993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.110957 restraints weight = 28204.023| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.67 r_work: 0.3048 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 24674 Z= 0.110 Angle : 0.530 6.444 33500 Z= 0.288 Chirality : 0.043 0.152 3878 Planarity : 0.004 0.044 4288 Dihedral : 6.636 59.926 3581 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 2.54 % Allowed : 16.85 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -1.93 (0.14), residues: 3258 helix: -0.12 (0.15), residues: 1052 sheet: -0.98 (0.20), residues: 666 loop : -2.26 (0.14), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 296 TYR 0.025 0.001 TYR D 300 PHE 0.013 0.001 PHE D 299 TRP 0.004 0.001 TRP A 542 HIS 0.005 0.001 HIS E 93 Details of bonding type rmsd covalent geometry : bond 0.00223 (24674) covalent geometry : angle 0.52968 (33500) hydrogen bonds : bond 0.04115 ( 933) hydrogen bonds : angle 4.78182 ( 2673) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 222 time to evaluate : 0.738 Fit side-chains REVERT: A 384 LYS cc_start: 0.8634 (mtpp) cc_final: 0.8272 (mttm) REVERT: B 194 LYS cc_start: 0.6236 (mmmt) cc_final: 0.5945 (tttp) REVERT: B 414 PHE cc_start: 0.9064 (OUTLIER) cc_final: 0.8216 (p90) REVERT: B 507 MET cc_start: 0.9385 (mmm) cc_final: 0.9054 (mmp) REVERT: C 93 HIS cc_start: 0.7772 (t70) cc_final: 0.7516 (t-90) REVERT: C 240 LYS cc_start: 0.8243 (tptt) cc_final: 0.7558 (ttmm) REVERT: C 548 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8357 (mp0) REVERT: C 619 ASP cc_start: 0.7278 (OUTLIER) cc_final: 0.6901 (m-30) REVERT: D 93 HIS cc_start: 0.7732 (t70) cc_final: 0.7445 (t-90) REVERT: D 240 LYS cc_start: 0.8113 (tptt) cc_final: 0.7489 (ttmm) REVERT: D 384 LYS cc_start: 0.8532 (mtpp) cc_final: 0.8110 (mttm) REVERT: F 226 HIS cc_start: 0.7372 (OUTLIER) cc_final: 0.7024 (m170) REVERT: F 384 LYS cc_start: 0.8593 (mtpp) cc_final: 0.8229 (mttt) REVERT: F 412 MET cc_start: 0.9168 (mmp) cc_final: 0.8945 (mmm) REVERT: F 414 PHE cc_start: 0.9010 (OUTLIER) cc_final: 0.8127 (p90) outliers start: 62 outliers final: 28 residues processed: 273 average time/residue: 0.5571 time to fit residues: 176.9441 Evaluate side-chains 236 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 204 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 414 PHE Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 455 TYR Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 619 ASP Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 455 TYR Chi-restraints excluded: chain D residue 533 SER Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 455 TYR Chi-restraints excluded: chain E residue 533 SER Chi-restraints excluded: chain F residue 111 CYS Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain F residue 226 HIS Chi-restraints excluded: chain F residue 414 PHE Chi-restraints excluded: chain F residue 455 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 223 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 150 optimal weight: 7.9990 chunk 172 optimal weight: 0.0670 chunk 88 optimal weight: 2.9990 chunk 289 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 overall best weight: 2.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 363 ASN B 473 ASN F 363 ASN F 473 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.139551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.108244 restraints weight = 28199.864| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.66 r_work: 0.2980 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 24674 Z= 0.150 Angle : 0.555 6.553 33500 Z= 0.301 Chirality : 0.044 0.194 3878 Planarity : 0.003 0.046 4288 Dihedral : 5.789 59.710 3498 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 3.36 % Allowed : 17.14 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -1.38 (0.14), residues: 3258 helix: 0.42 (0.16), residues: 1044 sheet: -0.76 (0.20), residues: 666 loop : -1.95 (0.14), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 479 TYR 0.028 0.002 TYR C 300 PHE 0.016 0.002 PHE C 299 TRP 0.006 0.001 TRP C 587 HIS 0.006 0.001 HIS E 93 Details of bonding type rmsd covalent geometry : bond 0.00345 (24674) covalent geometry : angle 0.55547 (33500) hydrogen bonds : bond 0.04557 ( 933) hydrogen bonds : angle 4.70930 ( 2673) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 201 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: A 384 LYS cc_start: 0.8641 (mtpp) cc_final: 0.8295 (mttt) REVERT: A 414 PHE cc_start: 0.9169 (OUTLIER) cc_final: 0.8103 (p90) REVERT: A 600 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8179 (mmtt) REVERT: B 414 PHE cc_start: 0.9138 (OUTLIER) cc_final: 0.8269 (p90) REVERT: C 93 HIS cc_start: 0.7826 (t70) cc_final: 0.7544 (t-90) REVERT: C 115 GLU cc_start: 0.4795 (OUTLIER) cc_final: 0.4433 (mm-30) REVERT: C 122 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8429 (mt) REVERT: C 240 LYS cc_start: 0.8210 (tptt) cc_final: 0.7514 (ttmm) REVERT: C 548 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8349 (mp0) REVERT: C 600 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8141 (mmtt) REVERT: C 619 ASP cc_start: 0.7257 (OUTLIER) cc_final: 0.6903 (m-30) REVERT: D 93 HIS cc_start: 0.7787 (t70) cc_final: 0.7491 (t-90) REVERT: D 122 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8316 (mt) REVERT: D 240 LYS cc_start: 0.8060 (tptt) cc_final: 0.7425 (ttmm) REVERT: D 416 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8456 (ppp) REVERT: D 548 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7916 (tp30) REVERT: E 414 PHE cc_start: 0.9225 (OUTLIER) cc_final: 0.8180 (p90) REVERT: F 412 MET cc_start: 0.9237 (mmp) cc_final: 0.8941 (mmm) REVERT: F 414 PHE cc_start: 0.9118 (OUTLIER) cc_final: 0.8251 (p90) REVERT: F 548 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8077 (tt0) REVERT: F 600 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8202 (mmtt) outliers start: 82 outliers final: 38 residues processed: 258 average time/residue: 0.5464 time to fit residues: 165.6556 Evaluate side-chains 239 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 187 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 414 PHE Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 455 TYR Chi-restraints excluded: chain C residue 600 LYS Chi-restraints excluded: chain C residue 619 ASP Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 190 ASN Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 414 PHE Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain D residue 455 TYR Chi-restraints excluded: chain D residue 548 GLU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 414 PHE Chi-restraints excluded: chain E residue 455 TYR Chi-restraints excluded: chain E residue 533 SER Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 111 CYS Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 414 PHE Chi-restraints excluded: chain F residue 455 TYR Chi-restraints excluded: chain F residue 548 GLU Chi-restraints excluded: chain F residue 600 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 8.9990 chunk 187 optimal weight: 6.9990 chunk 229 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 240 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 308 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 266 optimal weight: 3.9990 chunk 315 optimal weight: 4.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.138813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.107427 restraints weight = 28125.315| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.66 r_work: 0.2973 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 24674 Z= 0.173 Angle : 0.569 6.729 33500 Z= 0.309 Chirality : 0.045 0.190 3878 Planarity : 0.004 0.047 4288 Dihedral : 5.837 59.937 3498 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 3.85 % Allowed : 16.65 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -1.20 (0.14), residues: 3258 helix: 0.59 (0.16), residues: 1044 sheet: -0.82 (0.20), residues: 689 loop : -1.78 (0.15), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 610 TYR 0.029 0.002 TYR D 300 PHE 0.017 0.002 PHE D 299 TRP 0.006 0.001 TRP D 587 HIS 0.006 0.001 HIS E 93 Details of bonding type rmsd covalent geometry : bond 0.00404 (24674) covalent geometry : angle 0.56943 (33500) hydrogen bonds : bond 0.04687 ( 933) hydrogen bonds : angle 4.68704 ( 2673) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 206 time to evaluate : 0.676 Fit side-chains revert: symmetry clash REVERT: A 414 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.8086 (p90) REVERT: A 600 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8169 (mmtt) REVERT: B 122 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8359 (mt) REVERT: B 226 HIS cc_start: 0.7592 (OUTLIER) cc_final: 0.7311 (m170) REVERT: B 414 PHE cc_start: 0.9137 (OUTLIER) cc_final: 0.8270 (p90) REVERT: C 93 HIS cc_start: 0.7854 (t70) cc_final: 0.7577 (t-90) REVERT: C 115 GLU cc_start: 0.4732 (OUTLIER) cc_final: 0.4416 (mm-30) REVERT: C 122 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8415 (mt) REVERT: C 240 LYS cc_start: 0.8125 (tptt) cc_final: 0.7485 (ttmm) REVERT: C 584 ASN cc_start: 0.7987 (t0) cc_final: 0.7600 (t0) REVERT: C 600 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7829 (mptt) REVERT: C 619 ASP cc_start: 0.7182 (OUTLIER) cc_final: 0.6804 (m-30) REVERT: D 93 HIS cc_start: 0.7812 (t70) cc_final: 0.7520 (t-90) REVERT: D 122 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8296 (mt) REVERT: D 194 LYS cc_start: 0.7096 (OUTLIER) cc_final: 0.6889 (tttm) REVERT: D 240 LYS cc_start: 0.8088 (tptt) cc_final: 0.7395 (ttmm) REVERT: D 416 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8457 (ppp) REVERT: E 226 HIS cc_start: 0.7297 (OUTLIER) cc_final: 0.7016 (m-70) REVERT: E 414 PHE cc_start: 0.9169 (OUTLIER) cc_final: 0.8138 (p90) REVERT: F 226 HIS cc_start: 0.7410 (OUTLIER) cc_final: 0.7127 (m170) REVERT: F 275 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8462 (mm) REVERT: F 412 MET cc_start: 0.9259 (mmp) cc_final: 0.8951 (mmm) REVERT: F 414 PHE cc_start: 0.9109 (OUTLIER) cc_final: 0.8289 (p90) REVERT: F 548 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8036 (tt0) REVERT: F 600 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.7971 (mptt) outliers start: 94 outliers final: 49 residues processed: 274 average time/residue: 0.5488 time to fit residues: 177.0337 Evaluate side-chains 265 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 197 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 226 HIS Chi-restraints excluded: chain B residue 414 PHE Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain C residue 455 TYR Chi-restraints excluded: chain C residue 600 LYS Chi-restraints excluded: chain C residue 619 ASP Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 190 ASN Chi-restraints excluded: chain D residue 194 LYS Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 414 PHE Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain D residue 455 TYR Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 226 HIS Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain E residue 414 PHE Chi-restraints excluded: chain E residue 455 TYR Chi-restraints excluded: chain E residue 531 SER Chi-restraints excluded: chain E residue 533 SER Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 111 CYS Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 226 HIS Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 414 PHE Chi-restraints excluded: chain F residue 455 TYR Chi-restraints excluded: chain F residue 548 GLU Chi-restraints excluded: chain F residue 600 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 192 optimal weight: 8.9990 chunk 284 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 237 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 363 ASN C 330 GLN D 330 GLN F 363 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.140138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.108779 restraints weight = 28041.413| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.66 r_work: 0.2988 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 24674 Z= 0.140 Angle : 0.536 6.416 33500 Z= 0.291 Chirality : 0.044 0.209 3878 Planarity : 0.003 0.046 4288 Dihedral : 5.613 59.688 3497 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 3.85 % Allowed : 17.06 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -1.03 (0.14), residues: 3258 helix: 0.77 (0.16), residues: 1045 sheet: -0.79 (0.20), residues: 693 loop : -1.68 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 610 TYR 0.027 0.002 TYR C 300 PHE 0.015 0.002 PHE E 299 TRP 0.005 0.001 TRP C 587 HIS 0.005 0.001 HIS E 93 Details of bonding type rmsd covalent geometry : bond 0.00322 (24674) covalent geometry : angle 0.53570 (33500) hydrogen bonds : bond 0.04279 ( 933) hydrogen bonds : angle 4.50513 ( 2673) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 200 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 414 PHE cc_start: 0.9162 (OUTLIER) cc_final: 0.8059 (p90) REVERT: A 600 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8133 (mmtt) REVERT: B 98 ASP cc_start: 0.7867 (OUTLIER) cc_final: 0.7586 (p0) REVERT: B 122 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8355 (mt) REVERT: B 226 HIS cc_start: 0.7454 (OUTLIER) cc_final: 0.7197 (m170) REVERT: B 414 PHE cc_start: 0.9111 (OUTLIER) cc_final: 0.8287 (p90) REVERT: B 507 MET cc_start: 0.9383 (mmm) cc_final: 0.9091 (mmp) REVERT: C 93 HIS cc_start: 0.7801 (t70) cc_final: 0.7511 (t-90) REVERT: C 115 GLU cc_start: 0.4716 (OUTLIER) cc_final: 0.4391 (mm-30) REVERT: C 122 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8397 (mt) REVERT: C 240 LYS cc_start: 0.8093 (tptt) cc_final: 0.7444 (ttmm) REVERT: C 584 ASN cc_start: 0.8020 (t0) cc_final: 0.7551 (t0) REVERT: C 619 ASP cc_start: 0.7135 (OUTLIER) cc_final: 0.6767 (m-30) REVERT: D 93 HIS cc_start: 0.7770 (t70) cc_final: 0.7461 (t-90) REVERT: D 122 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8255 (mt) REVERT: D 240 LYS cc_start: 0.7979 (tptt) cc_final: 0.7257 (ttmm) REVERT: E 414 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.8053 (p90) REVERT: F 226 HIS cc_start: 0.7385 (OUTLIER) cc_final: 0.7133 (m170) REVERT: F 275 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8445 (mm) REVERT: F 412 MET cc_start: 0.9231 (mmp) cc_final: 0.8956 (mmm) REVERT: F 414 PHE cc_start: 0.9097 (OUTLIER) cc_final: 0.8298 (p90) outliers start: 94 outliers final: 47 residues processed: 264 average time/residue: 0.5298 time to fit residues: 164.3551 Evaluate side-chains 247 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 186 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 226 HIS Chi-restraints excluded: chain B residue 414 PHE Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain C residue 455 TYR Chi-restraints excluded: chain C residue 619 ASP Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 190 ASN Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 414 PHE Chi-restraints excluded: chain D residue 455 TYR Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 414 PHE Chi-restraints excluded: chain E residue 455 TYR Chi-restraints excluded: chain E residue 533 SER Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 226 HIS Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 414 PHE Chi-restraints excluded: chain F residue 455 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 161 optimal weight: 2.9990 chunk 129 optimal weight: 0.2980 chunk 275 optimal weight: 20.0000 chunk 234 optimal weight: 0.9980 chunk 8 optimal weight: 30.0000 chunk 304 optimal weight: 7.9990 chunk 257 optimal weight: 8.9990 chunk 121 optimal weight: 10.0000 chunk 271 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 177 optimal weight: 4.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 330 GLN D 330 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.139715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.108331 restraints weight = 28065.193| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.66 r_work: 0.2987 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 24674 Z= 0.152 Angle : 0.547 6.403 33500 Z= 0.296 Chirality : 0.044 0.210 3878 Planarity : 0.003 0.046 4288 Dihedral : 5.590 59.999 3495 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 3.73 % Allowed : 17.38 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -0.96 (0.15), residues: 3258 helix: 0.81 (0.16), residues: 1045 sheet: -0.74 (0.20), residues: 697 loop : -1.61 (0.15), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 610 TYR 0.028 0.002 TYR C 300 PHE 0.016 0.002 PHE D 299 TRP 0.006 0.001 TRP C 587 HIS 0.004 0.001 HIS E 93 Details of bonding type rmsd covalent geometry : bond 0.00354 (24674) covalent geometry : angle 0.54728 (33500) hydrogen bonds : bond 0.04424 ( 933) hydrogen bonds : angle 4.52020 ( 2673) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 194 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7897 (mp0) REVERT: A 414 PHE cc_start: 0.9175 (OUTLIER) cc_final: 0.8134 (p90) REVERT: A 600 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8172 (mmtt) REVERT: B 122 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8419 (mt) REVERT: B 166 GLU cc_start: 0.4769 (OUTLIER) cc_final: 0.3027 (tp30) REVERT: B 226 HIS cc_start: 0.7457 (OUTLIER) cc_final: 0.7201 (m170) REVERT: B 414 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8286 (p90) REVERT: B 507 MET cc_start: 0.9393 (mmm) cc_final: 0.9089 (mmp) REVERT: C 93 HIS cc_start: 0.7844 (t70) cc_final: 0.7574 (t-90) REVERT: C 115 GLU cc_start: 0.4770 (OUTLIER) cc_final: 0.4436 (mm-30) REVERT: C 122 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8437 (mt) REVERT: C 240 LYS cc_start: 0.8126 (tptt) cc_final: 0.7505 (ttmm) REVERT: C 563 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8933 (pt) REVERT: C 619 ASP cc_start: 0.7160 (OUTLIER) cc_final: 0.6769 (m-30) REVERT: D 93 HIS cc_start: 0.7773 (t70) cc_final: 0.7466 (t-90) REVERT: D 122 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8297 (mt) REVERT: D 240 LYS cc_start: 0.8020 (tptt) cc_final: 0.7322 (ttmm) REVERT: D 416 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8428 (ppp) REVERT: D 563 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8934 (pt) REVERT: D 584 ASN cc_start: 0.8035 (t0) cc_final: 0.7560 (t0) REVERT: E 414 PHE cc_start: 0.9163 (OUTLIER) cc_final: 0.8079 (p90) REVERT: F 226 HIS cc_start: 0.7456 (OUTLIER) cc_final: 0.7205 (m170) REVERT: F 275 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8483 (mm) REVERT: F 412 MET cc_start: 0.9261 (mmp) cc_final: 0.8994 (mmm) REVERT: F 414 PHE cc_start: 0.9121 (OUTLIER) cc_final: 0.8304 (p90) outliers start: 91 outliers final: 51 residues processed: 260 average time/residue: 0.5438 time to fit residues: 166.4616 Evaluate side-chains 262 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 193 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 226 HIS Chi-restraints excluded: chain B residue 414 PHE Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain C residue 455 TYR Chi-restraints excluded: chain C residue 563 ILE Chi-restraints excluded: chain C residue 619 ASP Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 190 ASN Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 226 HIS Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 414 PHE Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain D residue 455 TYR Chi-restraints excluded: chain D residue 563 ILE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 414 PHE Chi-restraints excluded: chain E residue 455 TYR Chi-restraints excluded: chain E residue 531 SER Chi-restraints excluded: chain E residue 533 SER Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 111 CYS Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 226 HIS Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 414 PHE Chi-restraints excluded: chain F residue 455 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 81 optimal weight: 0.9980 chunk 253 optimal weight: 4.9990 chunk 212 optimal weight: 0.4980 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 291 optimal weight: 0.0980 chunk 315 optimal weight: 4.9990 chunk 156 optimal weight: 6.9990 chunk 186 optimal weight: 4.9990 chunk 239 optimal weight: 7.9990 chunk 228 optimal weight: 9.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.140539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.109085 restraints weight = 28056.183| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.67 r_work: 0.2999 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 24674 Z= 0.136 Angle : 0.529 6.563 33500 Z= 0.287 Chirality : 0.043 0.229 3878 Planarity : 0.003 0.046 4288 Dihedral : 5.369 59.859 3492 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 3.53 % Allowed : 17.75 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -0.71 (0.15), residues: 3258 helix: 1.04 (0.16), residues: 1017 sheet: -0.65 (0.20), residues: 693 loop : -1.42 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 610 TYR 0.027 0.002 TYR C 300 PHE 0.015 0.002 PHE E 299 TRP 0.005 0.001 TRP D 587 HIS 0.004 0.001 HIS E 93 Details of bonding type rmsd covalent geometry : bond 0.00312 (24674) covalent geometry : angle 0.52868 (33500) hydrogen bonds : bond 0.04189 ( 933) hydrogen bonds : angle 4.41578 ( 2673) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 203 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7877 (mp0) REVERT: A 414 PHE cc_start: 0.9163 (OUTLIER) cc_final: 0.8075 (p90) REVERT: A 600 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8157 (mmtt) REVERT: B 98 ASP cc_start: 0.7872 (p0) cc_final: 0.7664 (p0) REVERT: B 122 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8427 (mt) REVERT: B 166 GLU cc_start: 0.4771 (OUTLIER) cc_final: 0.3138 (tp30) REVERT: B 226 HIS cc_start: 0.7249 (OUTLIER) cc_final: 0.7018 (m170) REVERT: B 414 PHE cc_start: 0.9124 (OUTLIER) cc_final: 0.8312 (p90) REVERT: C 93 HIS cc_start: 0.7815 (t70) cc_final: 0.7527 (t-90) REVERT: C 122 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8456 (mt) REVERT: C 240 LYS cc_start: 0.8103 (tptt) cc_final: 0.7478 (ttmm) REVERT: C 412 MET cc_start: 0.9267 (mmp) cc_final: 0.8990 (mmm) REVERT: C 619 ASP cc_start: 0.7154 (OUTLIER) cc_final: 0.6780 (m-30) REVERT: D 93 HIS cc_start: 0.7778 (t70) cc_final: 0.7469 (t-90) REVERT: D 122 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8286 (mt) REVERT: D 240 LYS cc_start: 0.8002 (tptt) cc_final: 0.7307 (ttmm) REVERT: D 412 MET cc_start: 0.9286 (mmp) cc_final: 0.8998 (mmm) REVERT: D 416 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.8450 (ppp) REVERT: E 414 PHE cc_start: 0.9168 (OUTLIER) cc_final: 0.8121 (p90) REVERT: F 226 HIS cc_start: 0.7220 (OUTLIER) cc_final: 0.6996 (m170) REVERT: F 275 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8467 (mm) REVERT: F 412 MET cc_start: 0.9230 (mmp) cc_final: 0.8955 (mmm) REVERT: F 414 PHE cc_start: 0.9104 (OUTLIER) cc_final: 0.8267 (p90) outliers start: 86 outliers final: 50 residues processed: 263 average time/residue: 0.5215 time to fit residues: 162.3928 Evaluate side-chains 256 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 191 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 226 HIS Chi-restraints excluded: chain B residue 414 PHE Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 226 HIS Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain C residue 455 TYR Chi-restraints excluded: chain C residue 619 ASP Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 226 HIS Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 414 PHE Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain D residue 455 TYR Chi-restraints excluded: chain D residue 565 SER Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 414 PHE Chi-restraints excluded: chain E residue 455 TYR Chi-restraints excluded: chain E residue 533 SER Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 211 GLU Chi-restraints excluded: chain F residue 226 HIS Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 414 PHE Chi-restraints excluded: chain F residue 455 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 183 optimal weight: 0.0770 chunk 256 optimal weight: 1.9990 chunk 229 optimal weight: 9.9990 chunk 159 optimal weight: 0.9990 chunk 54 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 262 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 314 optimal weight: 7.9990 chunk 160 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 overall best weight: 0.9344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.143366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.111898 restraints weight = 28049.244| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.67 r_work: 0.3034 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 24674 Z= 0.098 Angle : 0.488 7.296 33500 Z= 0.265 Chirality : 0.042 0.216 3878 Planarity : 0.003 0.045 4288 Dihedral : 5.055 59.385 3492 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 2.75 % Allowed : 18.98 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -0.49 (0.15), residues: 3258 helix: 1.26 (0.16), residues: 1017 sheet: -0.53 (0.20), residues: 689 loop : -1.31 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 479 TYR 0.024 0.001 TYR C 300 PHE 0.012 0.001 PHE E 299 TRP 0.004 0.001 TRP E 541 HIS 0.004 0.001 HIS E 93 Details of bonding type rmsd covalent geometry : bond 0.00214 (24674) covalent geometry : angle 0.48785 (33500) hydrogen bonds : bond 0.03630 ( 933) hydrogen bonds : angle 4.17676 ( 2673) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 201 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7863 (mp0) REVERT: A 600 LYS cc_start: 0.8397 (mptt) cc_final: 0.8177 (mmtp) REVERT: B 98 ASP cc_start: 0.7806 (p0) cc_final: 0.7588 (p0) REVERT: B 122 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8364 (mt) REVERT: B 226 HIS cc_start: 0.7374 (OUTLIER) cc_final: 0.7153 (m170) REVERT: B 414 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.8244 (p90) REVERT: B 600 LYS cc_start: 0.8504 (mmtt) cc_final: 0.8300 (mptt) REVERT: C 93 HIS cc_start: 0.7652 (t70) cc_final: 0.7369 (t-90) REVERT: C 122 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8405 (mt) REVERT: C 240 LYS cc_start: 0.8152 (tptt) cc_final: 0.7485 (ttmm) REVERT: C 261 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7775 (pm20) REVERT: C 619 ASP cc_start: 0.7066 (OUTLIER) cc_final: 0.6677 (m-30) REVERT: D 87 THR cc_start: 0.8654 (p) cc_final: 0.8425 (t) REVERT: D 93 HIS cc_start: 0.7634 (t70) cc_final: 0.7310 (t-90) REVERT: D 122 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8227 (mt) REVERT: D 240 LYS cc_start: 0.8045 (tptt) cc_final: 0.7265 (ttmm) REVERT: D 261 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7793 (pm20) REVERT: D 548 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7716 (tp30) REVERT: E 198 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.7027 (mt) REVERT: E 414 PHE cc_start: 0.9106 (OUTLIER) cc_final: 0.8025 (p90) REVERT: F 226 HIS cc_start: 0.7108 (OUTLIER) cc_final: 0.6907 (m170) REVERT: F 275 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8412 (mm) REVERT: F 412 MET cc_start: 0.9131 (mmp) cc_final: 0.8904 (mmm) REVERT: F 414 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.8181 (p90) outliers start: 67 outliers final: 38 residues processed: 247 average time/residue: 0.5167 time to fit residues: 150.1438 Evaluate side-chains 238 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 187 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 226 HIS Chi-restraints excluded: chain B residue 414 PHE Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 226 HIS Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 455 TYR Chi-restraints excluded: chain C residue 619 ASP Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 226 HIS Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 455 TYR Chi-restraints excluded: chain D residue 548 GLU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 414 PHE Chi-restraints excluded: chain E residue 533 SER Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 226 HIS Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 414 PHE Chi-restraints excluded: chain F residue 455 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 270 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 212 optimal weight: 0.7980 chunk 116 optimal weight: 30.0000 chunk 276 optimal weight: 40.0000 chunk 141 optimal weight: 0.9980 chunk 135 optimal weight: 9.9990 chunk 200 optimal weight: 9.9990 chunk 150 optimal weight: 6.9990 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 363 ASN E 252 HIS F 363 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.137680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.106230 restraints weight = 28249.222| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.66 r_work: 0.2953 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 24674 Z= 0.257 Angle : 0.629 8.590 33500 Z= 0.339 Chirality : 0.048 0.242 3878 Planarity : 0.004 0.049 4288 Dihedral : 5.737 59.639 3492 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 2.62 % Allowed : 19.19 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -0.90 (0.15), residues: 3258 helix: 0.68 (0.16), residues: 1051 sheet: -0.55 (0.20), residues: 690 loop : -1.53 (0.15), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 610 TYR 0.030 0.003 TYR D 300 PHE 0.020 0.003 PHE D 299 TRP 0.007 0.002 TRP E 542 HIS 0.007 0.002 HIS E 252 Details of bonding type rmsd covalent geometry : bond 0.00612 (24674) covalent geometry : angle 0.62910 (33500) hydrogen bonds : bond 0.05244 ( 933) hydrogen bonds : angle 4.73728 ( 2673) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 204 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8420 (mm110) REVERT: B 122 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8312 (mt) REVERT: B 166 GLU cc_start: 0.4703 (OUTLIER) cc_final: 0.3014 (tp30) REVERT: B 414 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.8301 (p90) REVERT: B 507 MET cc_start: 0.9373 (mmm) cc_final: 0.9063 (mmp) REVERT: B 548 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7833 (tp30) REVERT: C 93 HIS cc_start: 0.7878 (t70) cc_final: 0.7596 (t-90) REVERT: C 122 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8442 (mt) REVERT: C 240 LYS cc_start: 0.8143 (tptt) cc_final: 0.7474 (ttmm) REVERT: C 584 ASN cc_start: 0.8049 (t0) cc_final: 0.7664 (t0) REVERT: C 619 ASP cc_start: 0.7219 (OUTLIER) cc_final: 0.6832 (m-30) REVERT: D 122 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8326 (mt) REVERT: D 240 LYS cc_start: 0.8071 (tptt) cc_final: 0.7346 (ttmm) REVERT: D 548 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7828 (tp30) REVERT: D 584 ASN cc_start: 0.8044 (t0) cc_final: 0.7701 (t0) REVERT: E 414 PHE cc_start: 0.9189 (OUTLIER) cc_final: 0.8148 (p90) REVERT: F 275 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8500 (mm) REVERT: F 412 MET cc_start: 0.9264 (mmp) cc_final: 0.8955 (mmm) REVERT: F 414 PHE cc_start: 0.9152 (OUTLIER) cc_final: 0.8324 (p90) REVERT: F 548 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.7815 (tp30) outliers start: 64 outliers final: 38 residues processed: 254 average time/residue: 0.5461 time to fit residues: 162.3817 Evaluate side-chains 244 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 193 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 414 PHE Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 455 TYR Chi-restraints excluded: chain C residue 565 SER Chi-restraints excluded: chain C residue 619 ASP Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 455 TYR Chi-restraints excluded: chain D residue 548 GLU Chi-restraints excluded: chain D residue 565 SER Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 414 PHE Chi-restraints excluded: chain E residue 455 TYR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 414 PHE Chi-restraints excluded: chain F residue 455 TYR Chi-restraints excluded: chain F residue 548 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 98 optimal weight: 0.9990 chunk 182 optimal weight: 8.9990 chunk 320 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 chunk 162 optimal weight: 10.0000 chunk 180 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 185 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 ASN B 584 ASN E 333 ASN F 584 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.141914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.110456 restraints weight = 28044.321| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.67 r_work: 0.3017 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24674 Z= 0.111 Angle : 0.511 10.310 33500 Z= 0.277 Chirality : 0.043 0.222 3878 Planarity : 0.003 0.045 4288 Dihedral : 5.229 58.800 3492 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.01 % Allowed : 19.84 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -0.49 (0.15), residues: 3258 helix: 1.15 (0.16), residues: 1023 sheet: -0.44 (0.20), residues: 686 loop : -1.27 (0.16), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 296 TYR 0.025 0.002 TYR D 300 PHE 0.014 0.001 PHE D 299 TRP 0.004 0.001 TRP E 541 HIS 0.005 0.001 HIS E 93 Details of bonding type rmsd covalent geometry : bond 0.00247 (24674) covalent geometry : angle 0.51126 (33500) hydrogen bonds : bond 0.03870 ( 933) hydrogen bonds : angle 4.29721 ( 2673) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 193 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: A 261 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7858 (mp0) REVERT: A 600 LYS cc_start: 0.8361 (mptt) cc_final: 0.8122 (mmtt) REVERT: B 122 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8367 (mt) REVERT: B 414 PHE cc_start: 0.9064 (OUTLIER) cc_final: 0.8219 (p90) REVERT: C 93 HIS cc_start: 0.7753 (t70) cc_final: 0.7482 (t-90) REVERT: C 122 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8385 (mt) REVERT: C 240 LYS cc_start: 0.8109 (tptt) cc_final: 0.7472 (ttmm) REVERT: C 584 ASN cc_start: 0.7946 (t0) cc_final: 0.7519 (t0) REVERT: C 619 ASP cc_start: 0.7114 (OUTLIER) cc_final: 0.6741 (m-30) REVERT: D 93 HIS cc_start: 0.7692 (t70) cc_final: 0.7426 (t-90) REVERT: D 122 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8238 (mt) REVERT: D 240 LYS cc_start: 0.7952 (tptt) cc_final: 0.7225 (ttmm) REVERT: D 584 ASN cc_start: 0.7910 (t0) cc_final: 0.7568 (t0) REVERT: E 414 PHE cc_start: 0.9114 (OUTLIER) cc_final: 0.8053 (p90) REVERT: F 275 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8429 (mm) REVERT: F 412 MET cc_start: 0.9170 (mmp) cc_final: 0.8935 (mmm) REVERT: F 414 PHE cc_start: 0.9036 (OUTLIER) cc_final: 0.8226 (p90) outliers start: 49 outliers final: 37 residues processed: 232 average time/residue: 0.5244 time to fit residues: 143.5867 Evaluate side-chains 225 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 179 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 414 PHE Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 455 TYR Chi-restraints excluded: chain C residue 619 ASP Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 455 TYR Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 414 PHE Chi-restraints excluded: chain E residue 455 TYR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 414 PHE Chi-restraints excluded: chain F residue 455 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 238 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 220 optimal weight: 0.7980 chunk 229 optimal weight: 0.0870 chunk 183 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 282 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 179 optimal weight: 0.7980 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.143714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.112278 restraints weight = 28125.688| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.68 r_work: 0.3043 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24674 Z= 0.098 Angle : 0.491 10.114 33500 Z= 0.265 Chirality : 0.042 0.240 3878 Planarity : 0.003 0.044 4288 Dihedral : 4.978 59.317 3492 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 2.01 % Allowed : 19.84 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -0.34 (0.15), residues: 3258 helix: 1.33 (0.16), residues: 1030 sheet: -0.36 (0.21), residues: 687 loop : -1.24 (0.16), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 479 TYR 0.023 0.001 TYR D 300 PHE 0.013 0.001 PHE D 299 TRP 0.004 0.001 TRP E 541 HIS 0.005 0.001 HIS E 93 Details of bonding type rmsd covalent geometry : bond 0.00212 (24674) covalent geometry : angle 0.49067 (33500) hydrogen bonds : bond 0.03614 ( 933) hydrogen bonds : angle 4.12632 ( 2673) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7550.61 seconds wall clock time: 129 minutes 31.38 seconds (7771.38 seconds total)