Starting phenix.real_space_refine on Fri May 30 08:02:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k92_36972/05_2025/8k92_36972.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k92_36972/05_2025/8k92_36972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k92_36972/05_2025/8k92_36972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k92_36972/05_2025/8k92_36972.map" model { file = "/net/cci-nas-00/data/ceres_data/8k92_36972/05_2025/8k92_36972.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k92_36972/05_2025/8k92_36972.cif" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.034 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 P 6 5.49 5 S 48 5.16 5 C 21150 2.51 5 N 6000 2.21 5 O 6276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 33480 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5575 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "F" Number of atoms: 5575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5575 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "E" Number of atoms: 5575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5575 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "D" Number of atoms: 5575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5575 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "C" Number of atoms: 5575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5575 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "B" Number of atoms: 5575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5575 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'TS6': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'TS6': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'TS6': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'TS6': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'TS6': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'TS6': 1} Classifications: {'undetermined': 1} Time building chain proxies: 18.40, per 1000 atoms: 0.55 Number of scatterers: 33480 At special positions: 0 Unit cell: (137.76, 140.22, 163.18, 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) S 48 16.00 P 6 15.00 O 6276 8.00 N 6000 7.00 C 21150 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: 8.04 Conformation dependent library (CDL) restraints added in 4.3 seconds 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7920 Finding SS restraints... Secondary structure from input PDB file: 167 helices and 61 sheets defined 54.8% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.39 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 32 through 46 Processing helix chain 'A' and resid 58 through 69 removed outlier: 3.737A pdb=" N THR A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 119 removed outlier: 4.200A pdb=" N VAL A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASN A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ARG A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 153 Processing helix chain 'A' and resid 173 through 221 removed outlier: 3.696A pdb=" N ASN A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) Proline residue: A 216 - end of helix Processing helix chain 'A' and resid 224 through 242 Processing helix chain 'A' and resid 273 through 279 Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.760A pdb=" N GLN A 306 " --> pdb=" O HIS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 320 Processing helix chain 'A' and resid 322 through 333 Processing helix chain 'A' and resid 363 through 369 removed outlier: 3.717A pdb=" N GLY A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 379 removed outlier: 3.802A pdb=" N SER A 377 " --> pdb=" O ASP A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 407 Processing helix chain 'A' and resid 412 through 427 Processing helix chain 'A' and resid 436 through 452 removed outlier: 3.520A pdb=" N ILE A 440 " --> pdb=" O ARG A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 471 removed outlier: 3.900A pdb=" N SER A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 485 Processing helix chain 'A' and resid 531 through 535 Processing helix chain 'A' and resid 539 through 557 removed outlier: 3.645A pdb=" N TYR A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 597 Processing helix chain 'A' and resid 621 through 637 Processing helix chain 'A' and resid 649 through 654 removed outlier: 4.358A pdb=" N ALA A 652 " --> pdb=" O ALA A 649 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU A 654 " --> pdb=" O LEU A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 666 Processing helix chain 'A' and resid 676 through 686 Processing helix chain 'A' and resid 694 through 719 Processing helix chain 'F' and resid 4 through 8 Processing helix chain 'F' and resid 32 through 46 Processing helix chain 'F' and resid 58 through 70 removed outlier: 3.733A pdb=" N THR F 69 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN F 70 " --> pdb=" O TYR F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 111 removed outlier: 4.350A pdb=" N HIS F 100 " --> pdb=" O GLY F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 119 removed outlier: 3.837A pdb=" N PHE F 119 " --> pdb=" O LEU F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 154 Processing helix chain 'F' and resid 173 through 221 removed outlier: 3.985A pdb=" N ASN F 212 " --> pdb=" O HIS F 208 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG F 213 " --> pdb=" O TYR F 209 " (cutoff:3.500A) Proline residue: F 216 - end of helix Processing helix chain 'F' and resid 224 through 241 Processing helix chain 'F' and resid 246 through 250 removed outlier: 3.670A pdb=" N TRP F 250 " --> pdb=" O PRO F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 278 Processing helix chain 'F' and resid 293 through 295 No H-bonds generated for 'chain 'F' and resid 293 through 295' Processing helix chain 'F' and resid 302 through 306 removed outlier: 3.777A pdb=" N GLN F 306 " --> pdb=" O HIS F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 320 Processing helix chain 'F' and resid 322 through 333 Processing helix chain 'F' and resid 363 through 369 Processing helix chain 'F' and resid 373 through 380 removed outlier: 3.608A pdb=" N SER F 377 " --> pdb=" O ASP F 373 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU F 378 " --> pdb=" O PRO F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 408 Processing helix chain 'F' and resid 412 through 427 Processing helix chain 'F' and resid 436 through 451 removed outlier: 3.515A pdb=" N ILE F 440 " --> pdb=" O ARG F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 456 through 471 removed outlier: 3.752A pdb=" N SER F 471 " --> pdb=" O ARG F 467 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 484 Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 539 through 557 Processing helix chain 'F' and resid 583 through 597 Processing helix chain 'F' and resid 621 through 637 Processing helix chain 'F' and resid 649 through 651 No H-bonds generated for 'chain 'F' and resid 649 through 651' Processing helix chain 'F' and resid 657 through 666 Processing helix chain 'F' and resid 676 through 686 Processing helix chain 'F' and resid 694 through 719 Processing helix chain 'E' and resid 4 through 9 Processing helix chain 'E' and resid 32 through 46 Processing helix chain 'E' and resid 58 through 69 removed outlier: 3.587A pdb=" N THR E 69 " --> pdb=" O ALA E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 119 removed outlier: 4.555A pdb=" N HIS E 100 " --> pdb=" O GLY E 96 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL E 112 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ASN E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG E 114 " --> pdb=" O LEU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 154 Processing helix chain 'E' and resid 173 through 221 removed outlier: 3.509A pdb=" N ASN E 212 " --> pdb=" O HIS E 208 " (cutoff:3.500A) Proline residue: E 216 - end of helix Processing helix chain 'E' and resid 224 through 242 Processing helix chain 'E' and resid 273 through 279 Processing helix chain 'E' and resid 293 through 297 Processing helix chain 'E' and resid 302 through 306 removed outlier: 3.926A pdb=" N GLN E 306 " --> pdb=" O HIS E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 320 Processing helix chain 'E' and resid 322 through 332 Processing helix chain 'E' and resid 363 through 369 removed outlier: 3.722A pdb=" N GLY E 369 " --> pdb=" O GLU E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 379 removed outlier: 3.732A pdb=" N SER E 377 " --> pdb=" O ASP E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 407 Processing helix chain 'E' and resid 412 through 428 Processing helix chain 'E' and resid 436 through 452 Processing helix chain 'E' and resid 456 through 471 removed outlier: 3.812A pdb=" N SER E 471 " --> pdb=" O ARG E 467 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 485 Processing helix chain 'E' and resid 531 through 535 Processing helix chain 'E' and resid 539 through 557 removed outlier: 3.641A pdb=" N TYR E 557 " --> pdb=" O LEU E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 597 Processing helix chain 'E' and resid 621 through 637 Processing helix chain 'E' and resid 649 through 654 removed outlier: 4.492A pdb=" N ALA E 652 " --> pdb=" O ALA E 649 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU E 654 " --> pdb=" O LEU E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 657 through 666 Processing helix chain 'E' and resid 676 through 686 Processing helix chain 'E' and resid 694 through 719 Processing helix chain 'D' and resid 4 through 9 Processing helix chain 'D' and resid 32 through 46 Processing helix chain 'D' and resid 58 through 69 removed outlier: 3.671A pdb=" N THR D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 111 removed outlier: 4.420A pdb=" N HIS D 100 " --> pdb=" O GLY D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 118 Processing helix chain 'D' and resid 121 through 154 Processing helix chain 'D' and resid 173 through 221 removed outlier: 4.272A pdb=" N ASN D 212 " --> pdb=" O HIS D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 224 through 241 Processing helix chain 'D' and resid 273 through 278 Processing helix chain 'D' and resid 293 through 295 No H-bonds generated for 'chain 'D' and resid 293 through 295' Processing helix chain 'D' and resid 300 through 305 Processing helix chain 'D' and resid 314 through 320 Processing helix chain 'D' and resid 322 through 333 Processing helix chain 'D' and resid 363 through 369 Processing helix chain 'D' and resid 373 through 379 removed outlier: 3.653A pdb=" N SER D 377 " --> pdb=" O ASP D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 408 Processing helix chain 'D' and resid 412 through 427 Processing helix chain 'D' and resid 436 through 452 removed outlier: 3.566A pdb=" N ILE D 440 " --> pdb=" O ARG D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 471 removed outlier: 3.682A pdb=" N SER D 471 " --> pdb=" O ARG D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 531 through 535 Processing helix chain 'D' and resid 539 through 557 Processing helix chain 'D' and resid 583 through 597 Processing helix chain 'D' and resid 621 through 636 Processing helix chain 'D' and resid 649 through 651 No H-bonds generated for 'chain 'D' and resid 649 through 651' Processing helix chain 'D' and resid 657 through 666 Processing helix chain 'D' and resid 676 through 686 Processing helix chain 'D' and resid 694 through 719 Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 32 through 46 Processing helix chain 'C' and resid 58 through 69 removed outlier: 3.573A pdb=" N THR C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 119 removed outlier: 4.306A pdb=" N HIS C 100 " --> pdb=" O GLY C 96 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL C 112 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ASN C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 154 Processing helix chain 'C' and resid 173 through 221 removed outlier: 3.570A pdb=" N ALA C 206 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN C 212 " --> pdb=" O HIS C 208 " (cutoff:3.500A) Proline residue: C 216 - end of helix Processing helix chain 'C' and resid 224 through 241 Processing helix chain 'C' and resid 273 through 279 Processing helix chain 'C' and resid 293 through 295 No H-bonds generated for 'chain 'C' and resid 293 through 295' Processing helix chain 'C' and resid 302 through 306 removed outlier: 3.794A pdb=" N GLN C 306 " --> pdb=" O HIS C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 320 Processing helix chain 'C' and resid 322 through 333 Processing helix chain 'C' and resid 363 through 369 removed outlier: 3.977A pdb=" N GLY C 369 " --> pdb=" O GLU C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 379 removed outlier: 3.996A pdb=" N SER C 377 " --> pdb=" O ASP C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 407 Processing helix chain 'C' and resid 412 through 427 Processing helix chain 'C' and resid 436 through 452 removed outlier: 3.627A pdb=" N ILE C 440 " --> pdb=" O ARG C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 471 removed outlier: 3.892A pdb=" N SER C 471 " --> pdb=" O ARG C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 485 Processing helix chain 'C' and resid 531 through 535 Processing helix chain 'C' and resid 539 through 557 Processing helix chain 'C' and resid 583 through 597 Processing helix chain 'C' and resid 621 through 637 Processing helix chain 'C' and resid 649 through 654 removed outlier: 4.544A pdb=" N ALA C 652 " --> pdb=" O ALA C 649 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU C 654 " --> pdb=" O LEU C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 666 Processing helix chain 'C' and resid 676 through 686 Processing helix chain 'C' and resid 694 through 719 Processing helix chain 'B' and resid 4 through 8 Processing helix chain 'B' and resid 32 through 46 Processing helix chain 'B' and resid 58 through 69 removed outlier: 3.619A pdb=" N THR B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 111 Processing helix chain 'B' and resid 111 through 119 removed outlier: 3.599A pdb=" N PHE B 119 " --> pdb=" O LEU B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 154 Processing helix chain 'B' and resid 173 through 221 removed outlier: 4.064A pdb=" N ASN B 212 " --> pdb=" O HIS B 208 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG B 213 " --> pdb=" O TYR B 209 " (cutoff:3.500A) Proline residue: B 216 - end of helix Processing helix chain 'B' and resid 224 through 241 Processing helix chain 'B' and resid 246 through 251 removed outlier: 4.064A pdb=" N ARG B 251 " --> pdb=" O ALA B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 278 Processing helix chain 'B' and resid 293 through 297 removed outlier: 3.574A pdb=" N ILE B 297 " --> pdb=" O VAL B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 305 Processing helix chain 'B' and resid 314 through 320 Processing helix chain 'B' and resid 322 through 332 Processing helix chain 'B' and resid 363 through 369 removed outlier: 3.634A pdb=" N GLY B 369 " --> pdb=" O GLU B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 379 removed outlier: 3.930A pdb=" N SER B 377 " --> pdb=" O ASP B 373 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU B 378 " --> pdb=" O PRO B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 408 Processing helix chain 'B' and resid 412 through 427 Processing helix chain 'B' and resid 436 through 452 Processing helix chain 'B' and resid 456 through 471 removed outlier: 3.697A pdb=" N SER B 471 " --> pdb=" O ARG B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 484 Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 539 through 557 Processing helix chain 'B' and resid 583 through 597 Processing helix chain 'B' and resid 621 through 636 Processing helix chain 'B' and resid 649 through 654 removed outlier: 4.565A pdb=" N ALA B 652 " --> pdb=" O ALA B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 666 Processing helix chain 'B' and resid 676 through 686 Processing helix chain 'B' and resid 694 through 719 Processing sheet with id=AA1, first strand: chain 'A' and resid 266 through 269 removed outlier: 6.415A pdb=" N VAL A 267 " --> pdb=" O ILE A 311 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ASP A 313 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N GLU A 269 " --> pdb=" O ASP A 313 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N HIS A 48 " --> pdb=" O PHE A 380 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE A 382 " --> pdb=" O HIS A 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 88 through 93 Processing sheet with id=AA3, first strand: chain 'A' and resid 156 through 160 removed outlier: 4.036A pdb=" N ALA A 156 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR A 167 " --> pdb=" O ALA A 156 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU A 165 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG A 163 " --> pdb=" O ASN A 160 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 280 through 281 Processing sheet with id=AA5, first strand: chain 'A' and resid 284 through 286 removed outlier: 3.804A pdb=" N ASP A 286 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 289 " --> pdb=" O ASP A 286 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 389 through 391 Processing sheet with id=AA7, first strand: chain 'A' and resid 410 through 411 removed outlier: 7.057A pdb=" N GLN A 410 " --> pdb=" O LEU A 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 494 through 496 Processing sheet with id=AA9, first strand: chain 'A' and resid 498 through 504 removed outlier: 3.889A pdb=" N HIS A 527 " --> pdb=" O VAL A 565 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 604 through 606 removed outlier: 6.324A pdb=" N ALA A 605 " --> pdb=" O ILE A 645 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL A 644 " --> pdb=" O TYR A 672 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N VAL A 674 " --> pdb=" O VAL A 644 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU A 646 " --> pdb=" O VAL A 674 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 609 through 610 Processing sheet with id=AB3, first strand: chain 'F' and resid 266 through 269 removed outlier: 6.487A pdb=" N VAL F 267 " --> pdb=" O ILE F 311 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N ASP F 313 " --> pdb=" O VAL F 267 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N GLU F 269 " --> pdb=" O ASP F 313 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 253 through 254 removed outlier: 3.754A pdb=" N VAL F 88 " --> pdb=" O GLU F 348 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 156 through 159 Processing sheet with id=AB6, first strand: chain 'F' and resid 280 through 281 Processing sheet with id=AB7, first strand: chain 'F' and resid 284 through 286 Processing sheet with id=AB8, first strand: chain 'F' and resid 334 through 335 removed outlier: 3.943A pdb=" N VAL F 335 " --> pdb=" O PHE F 352 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE F 352 " --> pdb=" O VAL F 335 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'F' and resid 389 through 391 Processing sheet with id=AC1, first strand: chain 'F' and resid 410 through 411 removed outlier: 6.697A pdb=" N GLN F 410 " --> pdb=" O LEU F 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'F' and resid 494 through 496 Processing sheet with id=AC3, first strand: chain 'F' and resid 527 through 530 removed outlier: 3.881A pdb=" N HIS F 527 " --> pdb=" O VAL F 565 " (cutoff:3.500A) removed outlier: 9.663A pdb=" N GLU F 498 " --> pdb=" O LEU F 604 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N VAL F 606 " --> pdb=" O GLU F 498 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ASN F 500 " --> pdb=" O VAL F 606 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA F 605 " --> pdb=" O ILE F 645 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL F 644 " --> pdb=" O TYR F 672 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N VAL F 674 " --> pdb=" O VAL F 644 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU F 646 " --> pdb=" O VAL F 674 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 609 through 610 Processing sheet with id=AC5, first strand: chain 'E' and resid 266 through 269 removed outlier: 6.368A pdb=" N VAL E 267 " --> pdb=" O ILE E 311 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N ASP E 313 " --> pdb=" O VAL E 267 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N GLU E 269 " --> pdb=" O ASP E 313 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N HIS E 48 " --> pdb=" O PHE E 380 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE E 382 " --> pdb=" O HIS E 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 88 through 93 Processing sheet with id=AC7, first strand: chain 'E' and resid 156 through 160 removed outlier: 3.742A pdb=" N ALA E 156 " --> pdb=" O THR E 167 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR E 167 " --> pdb=" O ALA E 156 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER E 158 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU E 165 " --> pdb=" O SER E 158 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG E 163 " --> pdb=" O ASN E 160 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 284 through 286 removed outlier: 3.576A pdb=" N ASP E 286 " --> pdb=" O VAL E 289 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 389 through 391 Processing sheet with id=AD1, first strand: chain 'E' and resid 410 through 411 removed outlier: 7.174A pdb=" N GLN E 410 " --> pdb=" O LEU E 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'E' and resid 494 through 496 Processing sheet with id=AD3, first strand: chain 'E' and resid 527 through 530 removed outlier: 3.952A pdb=" N HIS E 527 " --> pdb=" O VAL E 565 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N LEU E 604 " --> pdb=" O GLU E 498 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASN E 500 " --> pdb=" O LEU E 604 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU E 502 " --> pdb=" O VAL E 606 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ALA E 605 " --> pdb=" O ILE E 645 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL E 644 " --> pdb=" O TYR E 672 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL E 674 " --> pdb=" O VAL E 644 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU E 646 " --> pdb=" O VAL E 674 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 609 through 610 Processing sheet with id=AD5, first strand: chain 'D' and resid 266 through 269 removed outlier: 6.400A pdb=" N VAL D 267 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ASP D 313 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N GLU D 269 " --> pdb=" O ASP D 313 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N HIS D 48 " --> pdb=" O PHE D 380 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE D 382 " --> pdb=" O HIS D 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 253 through 256 removed outlier: 3.606A pdb=" N LEU D 255 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N LEU D 78 " --> pdb=" O LEU D 255 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 156 through 159 Processing sheet with id=AD8, first strand: chain 'D' and resid 280 through 281 Processing sheet with id=AD9, first strand: chain 'D' and resid 334 through 335 Processing sheet with id=AE1, first strand: chain 'D' and resid 389 through 391 Processing sheet with id=AE2, first strand: chain 'D' and resid 410 through 411 removed outlier: 6.847A pdb=" N GLN D 410 " --> pdb=" O LEU D 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'D' and resid 494 through 496 Processing sheet with id=AE4, first strand: chain 'D' and resid 527 through 530 removed outlier: 3.954A pdb=" N HIS D 527 " --> pdb=" O VAL D 565 " (cutoff:3.500A) removed outlier: 9.594A pdb=" N GLU D 498 " --> pdb=" O LEU D 604 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N VAL D 606 " --> pdb=" O GLU D 498 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ASN D 500 " --> pdb=" O VAL D 606 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA D 605 " --> pdb=" O ILE D 645 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL D 644 " --> pdb=" O TYR D 672 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N VAL D 674 " --> pdb=" O VAL D 644 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU D 646 " --> pdb=" O VAL D 674 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 609 through 610 Processing sheet with id=AE6, first strand: chain 'C' and resid 266 through 269 removed outlier: 6.465A pdb=" N VAL C 267 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N ASP C 313 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N GLU C 269 " --> pdb=" O ASP C 313 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N HIS C 48 " --> pdb=" O PHE C 380 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 253 through 254 Processing sheet with id=AE8, first strand: chain 'C' and resid 156 through 160 removed outlier: 3.879A pdb=" N ALA C 156 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR C 167 " --> pdb=" O ALA C 156 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG C 163 " --> pdb=" O ASN C 160 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 280 through 281 Processing sheet with id=AF1, first strand: chain 'C' and resid 284 through 286 removed outlier: 3.703A pdb=" N ASP C 286 " --> pdb=" O VAL C 289 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 389 through 391 Processing sheet with id=AF3, first strand: chain 'C' and resid 410 through 411 removed outlier: 7.188A pdb=" N GLN C 410 " --> pdb=" O LEU C 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'C' and resid 494 through 496 Processing sheet with id=AF5, first strand: chain 'C' and resid 527 through 530 removed outlier: 4.083A pdb=" N HIS C 527 " --> pdb=" O VAL C 565 " (cutoff:3.500A) removed outlier: 9.458A pdb=" N GLU C 498 " --> pdb=" O LEU C 604 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N VAL C 606 " --> pdb=" O GLU C 498 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ASN C 500 " --> pdb=" O VAL C 606 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA C 605 " --> pdb=" O ILE C 645 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL C 644 " --> pdb=" O TYR C 672 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N VAL C 674 " --> pdb=" O VAL C 644 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU C 646 " --> pdb=" O VAL C 674 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 609 through 610 Processing sheet with id=AF7, first strand: chain 'B' and resid 266 through 269 removed outlier: 4.329A pdb=" N ASP B 313 " --> pdb=" O GLU B 269 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N HIS B 48 " --> pdb=" O PHE B 380 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE B 382 " --> pdb=" O HIS B 48 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 88 through 93 Processing sheet with id=AF9, first strand: chain 'B' and resid 156 through 159 Processing sheet with id=AG1, first strand: chain 'B' and resid 284 through 286 Processing sheet with id=AG2, first strand: chain 'B' and resid 334 through 335 removed outlier: 3.847A pdb=" N VAL B 335 " --> pdb=" O PHE B 352 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE B 352 " --> pdb=" O VAL B 335 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'B' and resid 389 through 391 Processing sheet with id=AG4, first strand: chain 'B' and resid 410 through 411 removed outlier: 6.851A pdb=" N GLN B 410 " --> pdb=" O LEU B 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'B' and resid 494 through 496 Processing sheet with id=AG6, first strand: chain 'B' and resid 527 through 530 removed outlier: 4.016A pdb=" N HIS B 527 " --> pdb=" O VAL B 565 " (cutoff:3.500A) removed outlier: 9.615A pdb=" N GLU B 498 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 9.035A pdb=" N VAL B 606 " --> pdb=" O GLU B 498 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ASN B 500 " --> pdb=" O VAL B 606 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ALA B 605 " --> pdb=" O ILE B 645 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL B 644 " --> pdb=" O TYR B 672 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N VAL B 674 " --> pdb=" O VAL B 644 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU B 646 " --> pdb=" O VAL B 674 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'B' and resid 609 through 610 1919 hydrogen bonds defined for protein. 5592 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: 13.88 Time building geometry restraints manager: 9.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 11711 1.36 - 1.51: 8835 1.51 - 1.65: 13516 1.65 - 1.80: 58 1.80 - 1.95: 20 Bond restraints: 34140 Sorted by residual: bond pdb=" P TS6 B 801 " pdb=" S2P TS6 B 801 " ideal model delta sigma weight residual 2.275 1.946 0.329 2.00e-02 2.50e+03 2.71e+02 bond pdb=" P TS6 F 801 " pdb=" S2P TS6 F 801 " ideal model delta sigma weight residual 2.275 1.947 0.328 2.00e-02 2.50e+03 2.70e+02 bond pdb=" P TS6 E 801 " pdb=" S2P TS6 E 801 " ideal model delta sigma weight residual 2.275 1.947 0.328 2.00e-02 2.50e+03 2.70e+02 bond pdb=" P TS6 D 801 " pdb=" S2P TS6 D 801 " ideal model delta sigma weight residual 2.275 1.947 0.328 2.00e-02 2.50e+03 2.69e+02 bond pdb=" P TS6 A 801 " pdb=" S2P TS6 A 801 " ideal model delta sigma weight residual 2.275 1.947 0.328 2.00e-02 2.50e+03 2.69e+02 ... (remaining 34135 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.46: 46159 3.46 - 6.93: 167 6.93 - 10.39: 5 10.39 - 13.85: 16 13.85 - 17.32: 9 Bond angle restraints: 46356 Sorted by residual: angle pdb=" CA PRO C 509 " pdb=" N PRO C 509 " pdb=" CD PRO C 509 " ideal model delta sigma weight residual 112.00 100.03 11.97 1.40e+00 5.10e-01 7.32e+01 angle pdb=" O1P TS6 A 801 " pdb=" P TS6 A 801 " pdb=" S2P TS6 A 801 " ideal model delta sigma weight residual 98.15 115.47 -17.32 3.00e+00 1.11e-01 3.33e+01 angle pdb=" O1P TS6 D 801 " pdb=" P TS6 D 801 " pdb=" S2P TS6 D 801 " ideal model delta sigma weight residual 98.15 115.30 -17.15 3.00e+00 1.11e-01 3.27e+01 angle pdb=" O1P TS6 F 801 " pdb=" P TS6 F 801 " pdb=" S2P TS6 F 801 " ideal model delta sigma weight residual 98.15 115.24 -17.09 3.00e+00 1.11e-01 3.25e+01 angle pdb=" O1P TS6 C 801 " pdb=" P TS6 C 801 " pdb=" S2P TS6 C 801 " ideal model delta sigma weight residual 98.15 115.22 -17.07 3.00e+00 1.11e-01 3.24e+01 ... (remaining 46351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 18752 17.95 - 35.91: 1501 35.91 - 53.86: 275 53.86 - 71.82: 110 71.82 - 89.77: 80 Dihedral angle restraints: 20718 sinusoidal: 8388 harmonic: 12330 Sorted by residual: dihedral pdb=" CA PHE E 692 " pdb=" C PHE E 692 " pdb=" N ARG E 693 " pdb=" CA ARG E 693 " ideal model delta harmonic sigma weight residual -180.00 -153.97 -26.03 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA PRO C 509 " pdb=" C PRO C 509 " pdb=" N TYR C 510 " pdb=" CA TYR C 510 " ideal model delta harmonic sigma weight residual -180.00 -155.35 -24.65 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA LEU D 411 " pdb=" C LEU D 411 " pdb=" N THR D 412 " pdb=" CA THR D 412 " ideal model delta harmonic sigma weight residual 180.00 160.08 19.92 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 20715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 4391 0.055 - 0.111: 681 0.111 - 0.166: 76 0.166 - 0.222: 12 0.222 - 0.277: 6 Chirality restraints: 5166 Sorted by residual: chirality pdb=" CB VAL C 438 " pdb=" CA VAL C 438 " pdb=" CG1 VAL C 438 " pdb=" CG2 VAL C 438 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB VAL E 438 " pdb=" CA VAL E 438 " pdb=" CG1 VAL E 438 " pdb=" CG2 VAL E 438 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB VAL D 438 " pdb=" CA VAL D 438 " pdb=" CG1 VAL D 438 " pdb=" CG2 VAL D 438 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 5163 not shown) Planarity restraints: 6186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 508 " -0.080 5.00e-02 4.00e+02 1.12e-01 2.01e+01 pdb=" N PRO C 509 " 0.194 5.00e-02 4.00e+02 pdb=" CA PRO C 509 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 509 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 363 " 0.046 5.00e-02 4.00e+02 6.94e-02 7.71e+00 pdb=" N PRO F 364 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO F 364 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 364 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 114 " -0.226 9.50e-02 1.11e+02 1.02e-01 6.70e+00 pdb=" NE ARG B 114 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG B 114 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 114 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 114 " -0.012 2.00e-02 2.50e+03 ... (remaining 6183 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 441 2.68 - 3.23: 32333 3.23 - 3.79: 55301 3.79 - 4.34: 71441 4.34 - 4.90: 121961 Nonbonded interactions: 281477 Sorted by model distance: nonbonded pdb=" OH TYR B 552 " pdb=" OE2 GLU B 678 " model vdw 2.122 3.040 nonbonded pdb=" NH1 ARG C 202 " pdb=" O ALA C 239 " model vdw 2.146 3.120 nonbonded pdb=" OG1 THR E 518 " pdb=" OE1 GLU E 572 " model vdw 2.159 3.040 nonbonded pdb=" OG1 THR F 518 " pdb=" OE2 GLU F 572 " model vdw 2.165 3.040 nonbonded pdb=" OH TYR A 5 " pdb=" OE2 GLU A 9 " model vdw 2.172 3.040 ... (remaining 281472 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 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: 0.030 Extract box with map and model: 1.260 Check model and map are aligned: 0.230 Set scattering table: 0.300 Process input model: 72.620 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.150 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 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 : 0.006 0.329 34140 Z= 0.319 Angle : 0.702 17.317 46356 Z= 0.371 Chirality : 0.042 0.277 5166 Planarity : 0.005 0.112 6186 Dihedral : 15.169 89.774 12798 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.44 % Favored : 96.49 % Rotamer: Outliers : 0.38 % Allowed : 0.41 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.13), residues: 4302 helix: 1.99 (0.11), residues: 2235 sheet: -0.28 (0.22), residues: 531 loop : -0.15 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 290 HIS 0.005 0.001 HIS A 60 PHE 0.029 0.001 PHE E 692 TYR 0.026 0.002 TYR E 271 ARG 0.018 0.001 ARG D 114 Details of bonding type rmsd hydrogen bonds : bond 0.14482 ( 1919) hydrogen bonds : angle 6.12849 ( 5592) covalent geometry : bond 0.00631 (34140) covalent geometry : angle 0.70195 (46356) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 176 time to evaluate : 3.409 Fit side-chains REVERT: A 57 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8629 (tt) REVERT: A 201 LEU cc_start: 0.8559 (mm) cc_final: 0.8237 (tp) REVERT: A 208 HIS cc_start: 0.7530 (m-70) cc_final: 0.7207 (m-70) REVERT: F 225 ARG cc_start: 0.8160 (mmm-85) cc_final: 0.7924 (mmm-85) REVERT: D 199 ARG cc_start: 0.7134 (mtp180) cc_final: 0.6817 (mmt90) REVERT: D 710 GLU cc_start: 0.7099 (tp30) cc_final: 0.6698 (tm-30) REVERT: C 57 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8522 (tt) REVERT: C 205 TRP cc_start: 0.5773 (t60) cc_final: 0.5544 (t-100) outliers start: 13 outliers final: 1 residues processed: 187 average time/residue: 0.4639 time to fit residues: 142.4799 Evaluate side-chains 126 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 123 time to evaluate : 3.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain B residue 57 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 359 optimal weight: 8.9990 chunk 322 optimal weight: 10.0000 chunk 179 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 217 optimal weight: 2.9990 chunk 172 optimal weight: 7.9990 chunk 333 optimal weight: 7.9990 chunk 129 optimal weight: 1.9990 chunk 203 optimal weight: 7.9990 chunk 248 optimal weight: 2.9990 chunk 386 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 642 GLN ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 ASN ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.128939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.095052 restraints weight = 59777.995| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.63 r_work: 0.3259 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 34140 Z= 0.225 Angle : 0.590 8.009 46356 Z= 0.298 Chirality : 0.041 0.180 5166 Planarity : 0.005 0.085 6186 Dihedral : 4.309 50.851 4806 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.25 % Favored : 96.68 % Rotamer: Outliers : 0.65 % Allowed : 5.58 % Favored : 93.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.13), residues: 4302 helix: 1.96 (0.11), residues: 2262 sheet: -0.28 (0.22), residues: 516 loop : -0.30 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 290 HIS 0.006 0.001 HIS C 543 PHE 0.031 0.002 PHE C 119 TYR 0.025 0.002 TYR E 50 ARG 0.010 0.001 ARG C 202 Details of bonding type rmsd hydrogen bonds : bond 0.04196 ( 1919) hydrogen bonds : angle 4.79515 ( 5592) covalent geometry : bond 0.00530 (34140) covalent geometry : angle 0.58962 (46356) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 3.731 Fit side-chains revert: symmetry clash REVERT: A 208 HIS cc_start: 0.7813 (m-70) cc_final: 0.7415 (m-70) REVERT: A 426 MET cc_start: 0.9166 (mtp) cc_final: 0.8954 (mtp) REVERT: F 214 PHE cc_start: 0.7433 (m-80) cc_final: 0.6269 (m-80) REVERT: F 218 PHE cc_start: 0.7271 (m-10) cc_final: 0.6883 (m-80) REVERT: F 225 ARG cc_start: 0.8448 (mmm-85) cc_final: 0.8122 (mmm-85) REVERT: F 611 ASP cc_start: 0.7416 (p0) cc_final: 0.7188 (p0) REVERT: E 56 SER cc_start: 0.9058 (m) cc_final: 0.8647 (t) REVERT: E 118 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7488 (mp) REVERT: E 572 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7245 (mt-10) REVERT: D 710 GLU cc_start: 0.7200 (tp30) cc_final: 0.6571 (tm-30) outliers start: 22 outliers final: 15 residues processed: 158 average time/residue: 0.4898 time to fit residues: 126.0132 Evaluate side-chains 143 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 3.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 703 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 579 GLU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 208 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 25 optimal weight: 6.9990 chunk 417 optimal weight: 0.9990 chunk 415 optimal weight: 5.9990 chunk 423 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 chunk 419 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 290 optimal weight: 0.9980 chunk 400 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN E 212 ASN ** E 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.130791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.097087 restraints weight = 59996.862| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.62 r_work: 0.3285 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 34140 Z= 0.132 Angle : 0.507 7.077 46356 Z= 0.255 Chirality : 0.038 0.141 5166 Planarity : 0.004 0.069 6186 Dihedral : 4.038 49.647 4804 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.91 % Favored : 97.02 % Rotamer: Outliers : 0.91 % Allowed : 7.38 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.13), residues: 4302 helix: 2.09 (0.11), residues: 2277 sheet: -0.22 (0.21), residues: 522 loop : -0.25 (0.16), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 205 HIS 0.004 0.001 HIS B 303 PHE 0.028 0.001 PHE C 119 TYR 0.019 0.001 TYR E 50 ARG 0.006 0.000 ARG C 202 Details of bonding type rmsd hydrogen bonds : bond 0.03678 ( 1919) hydrogen bonds : angle 4.43913 ( 5592) covalent geometry : bond 0.00302 (34140) covalent geometry : angle 0.50701 (46356) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 3.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 TRP cc_start: 0.7527 (t-100) cc_final: 0.7299 (t-100) REVERT: A 208 HIS cc_start: 0.7756 (m-70) cc_final: 0.7436 (m-70) REVERT: E 56 SER cc_start: 0.9063 (m) cc_final: 0.8704 (t) REVERT: E 572 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7234 (mt-10) REVERT: D 678 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7474 (mm-30) REVERT: D 710 GLU cc_start: 0.7150 (tp30) cc_final: 0.6559 (tm-30) REVERT: C 205 TRP cc_start: 0.6391 (t60) cc_final: 0.6190 (t-100) outliers start: 31 outliers final: 19 residues processed: 180 average time/residue: 0.4952 time to fit residues: 146.7557 Evaluate side-chains 150 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 3.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 566 THR Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain D residue 579 GLU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 208 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 193 optimal weight: 2.9990 chunk 308 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 239 optimal weight: 0.0370 chunk 400 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 18 optimal weight: 20.0000 chunk 339 optimal weight: 0.0470 chunk 331 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 573 GLN ** E 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.139395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.105481 restraints weight = 59552.564| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.55 r_work: 0.3297 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34140 Z= 0.119 Angle : 0.493 7.862 46356 Z= 0.246 Chirality : 0.037 0.138 5166 Planarity : 0.004 0.068 6186 Dihedral : 3.944 48.312 4804 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.95 % Favored : 96.98 % Rotamer: Outliers : 1.21 % Allowed : 8.44 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.13), residues: 4302 helix: 2.19 (0.11), residues: 2280 sheet: -0.26 (0.21), residues: 516 loop : -0.19 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 205 HIS 0.003 0.000 HIS B 303 PHE 0.017 0.001 PHE C 124 TYR 0.016 0.001 TYR D 209 ARG 0.005 0.000 ARG D 490 Details of bonding type rmsd hydrogen bonds : bond 0.03465 ( 1919) hydrogen bonds : angle 4.26802 ( 5592) covalent geometry : bond 0.00269 (34140) covalent geometry : angle 0.49255 (46356) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 143 time to evaluate : 3.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ARG cc_start: 0.8571 (mtm110) cc_final: 0.8170 (ptp90) REVERT: A 208 HIS cc_start: 0.7734 (m-70) cc_final: 0.7292 (m-70) REVERT: D 79 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8149 (pp) REVERT: D 710 GLU cc_start: 0.7138 (tp30) cc_final: 0.6625 (tm-30) REVERT: C 205 TRP cc_start: 0.6575 (t60) cc_final: 0.6248 (t-100) REVERT: B 708 ARG cc_start: 0.8029 (mmt-90) cc_final: 0.7769 (mmt-90) outliers start: 41 outliers final: 19 residues processed: 177 average time/residue: 0.4773 time to fit residues: 136.7417 Evaluate side-chains 144 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 3.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 566 THR Chi-restraints excluded: chain D residue 579 GLU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 208 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 75 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 173 optimal weight: 3.9990 chunk 425 optimal weight: 0.7980 chunk 273 optimal weight: 7.9990 chunk 203 optimal weight: 0.0370 chunk 277 optimal weight: 0.7980 chunk 118 optimal weight: 8.9990 chunk 72 optimal weight: 0.1980 chunk 413 optimal weight: 0.7980 chunk 156 optimal weight: 5.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 602 GLN F 573 GLN ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.141732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.108023 restraints weight = 59429.440| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.29 r_work: 0.3339 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 34140 Z= 0.093 Angle : 0.472 10.683 46356 Z= 0.233 Chirality : 0.037 0.158 5166 Planarity : 0.004 0.069 6186 Dihedral : 3.812 47.706 4804 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.67 % Favored : 97.26 % Rotamer: Outliers : 1.21 % Allowed : 9.23 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.13), residues: 4302 helix: 2.34 (0.11), residues: 2277 sheet: -0.17 (0.21), residues: 516 loop : -0.15 (0.16), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 205 HIS 0.003 0.000 HIS B 303 PHE 0.015 0.001 PHE D 352 TYR 0.016 0.001 TYR D 209 ARG 0.004 0.000 ARG D 287 Details of bonding type rmsd hydrogen bonds : bond 0.03276 ( 1919) hydrogen bonds : angle 4.07814 ( 5592) covalent geometry : bond 0.00199 (34140) covalent geometry : angle 0.47186 (46356) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 153 time to evaluate : 3.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.7682 (m-70) cc_final: 0.7253 (m-70) REVERT: F 79 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8543 (pp) REVERT: E 56 SER cc_start: 0.8899 (p) cc_final: 0.8378 (t) REVERT: D 79 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8109 (pp) REVERT: D 210 LEU cc_start: 0.6973 (mt) cc_final: 0.6607 (mt) REVERT: D 710 GLU cc_start: 0.7079 (tp30) cc_final: 0.6603 (tm-30) REVERT: C 205 TRP cc_start: 0.6510 (t60) cc_final: 0.6139 (t-100) REVERT: B 708 ARG cc_start: 0.7993 (mmt-90) cc_final: 0.7752 (mmt-90) outliers start: 41 outliers final: 24 residues processed: 188 average time/residue: 0.4576 time to fit residues: 141.9977 Evaluate side-chains 155 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 3.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 573 GLN Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 566 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 363 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 109 optimal weight: 0.9990 chunk 378 optimal weight: 5.9990 chunk 170 optimal weight: 7.9990 chunk 264 optimal weight: 7.9990 chunk 201 optimal weight: 4.9990 chunk 273 optimal weight: 8.9990 chunk 83 optimal weight: 30.0000 chunk 130 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 158 optimal weight: 50.0000 chunk 75 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 303 HIS F 653 ASN ** E 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.127654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.093710 restraints weight = 60493.892| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.64 r_work: 0.3232 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 34140 Z= 0.278 Angle : 0.609 9.577 46356 Z= 0.304 Chirality : 0.041 0.226 5166 Planarity : 0.005 0.066 6186 Dihedral : 4.116 51.884 4804 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.14 % Favored : 96.79 % Rotamer: Outliers : 1.73 % Allowed : 9.64 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.13), residues: 4302 helix: 2.03 (0.11), residues: 2280 sheet: -0.33 (0.21), residues: 501 loop : -0.28 (0.16), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 290 HIS 0.009 0.001 HIS C 543 PHE 0.018 0.002 PHE F 571 TYR 0.023 0.002 TYR C 420 ARG 0.006 0.001 ARG F 328 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 1919) hydrogen bonds : angle 4.35254 ( 5592) covalent geometry : bond 0.00661 (34140) covalent geometry : angle 0.60934 (46356) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 135 time to evaluate : 3.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.7740 (m-70) cc_final: 0.7322 (m-70) REVERT: F 218 PHE cc_start: 0.7280 (m-10) cc_final: 0.6748 (m-80) REVERT: F 225 ARG cc_start: 0.8435 (mmm-85) cc_final: 0.8181 (tpt90) REVERT: F 581 ASP cc_start: 0.8307 (p0) cc_final: 0.7698 (t0) REVERT: D 79 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8369 (pp) REVERT: D 201 LEU cc_start: 0.8642 (tp) cc_final: 0.8329 (tp) REVERT: D 710 GLU cc_start: 0.7201 (tp30) cc_final: 0.6690 (tm-30) REVERT: C 205 TRP cc_start: 0.6642 (t60) cc_final: 0.6323 (t-100) REVERT: B 484 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7326 (mp0) outliers start: 59 outliers final: 31 residues processed: 187 average time/residue: 0.4579 time to fit residues: 141.7052 Evaluate side-chains 165 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 3.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 578 ILE Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 566 THR Chi-restraints excluded: chain D residue 579 GLU Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 484 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 10 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 116 optimal weight: 6.9990 chunk 412 optimal weight: 6.9990 chunk 405 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 172 optimal weight: 3.9990 chunk 151 optimal weight: 7.9990 chunk 282 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.128639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.095004 restraints weight = 60420.095| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.63 r_work: 0.3260 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 34140 Z= 0.173 Angle : 0.531 10.818 46356 Z= 0.263 Chirality : 0.039 0.254 5166 Planarity : 0.004 0.067 6186 Dihedral : 4.055 51.173 4804 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.91 % Favored : 97.02 % Rotamer: Outliers : 1.50 % Allowed : 10.44 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.13), residues: 4302 helix: 2.07 (0.10), residues: 2286 sheet: -0.32 (0.21), residues: 501 loop : -0.28 (0.16), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 290 HIS 0.004 0.001 HIS C 543 PHE 0.013 0.001 PHE E 629 TYR 0.018 0.002 TYR E 50 ARG 0.007 0.000 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.03533 ( 1919) hydrogen bonds : angle 4.23549 ( 5592) covalent geometry : bond 0.00405 (34140) covalent geometry : angle 0.53093 (46356) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 133 time to evaluate : 3.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.7714 (m-70) cc_final: 0.7302 (m-70) REVERT: A 678 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8284 (tp30) REVERT: F 79 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8585 (pp) REVERT: F 689 MET cc_start: 0.8383 (mtp) cc_final: 0.8106 (mtp) REVERT: E 659 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7809 (pt0) REVERT: D 79 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8278 (pp) REVERT: D 201 LEU cc_start: 0.8659 (tp) cc_final: 0.8350 (tp) REVERT: D 710 GLU cc_start: 0.7166 (tp30) cc_final: 0.6692 (tm-30) REVERT: C 205 TRP cc_start: 0.6593 (t60) cc_final: 0.6302 (t-100) REVERT: B 334 GLN cc_start: 0.7371 (OUTLIER) cc_final: 0.7001 (tt0) REVERT: B 484 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7318 (mp0) REVERT: B 708 ARG cc_start: 0.7936 (mmt-90) cc_final: 0.7661 (mmt-90) outliers start: 51 outliers final: 41 residues processed: 177 average time/residue: 0.4652 time to fit residues: 135.3790 Evaluate side-chains 169 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 123 time to evaluate : 3.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 128 LYS Chi-restraints excluded: chain F residue 209 TYR Chi-restraints excluded: chain F residue 246 ASP Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain F residue 703 LEU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 659 GLU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 566 THR Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 613 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 130 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 407 optimal weight: 0.3980 chunk 235 optimal weight: 4.9990 chunk 376 optimal weight: 8.9990 chunk 147 optimal weight: 0.9990 chunk 424 optimal weight: 4.9990 chunk 224 optimal weight: 7.9990 chunk 388 optimal weight: 20.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 GLN ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.129613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.096077 restraints weight = 59673.939| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.62 r_work: 0.3275 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34140 Z= 0.142 Angle : 0.507 11.060 46356 Z= 0.251 Chirality : 0.038 0.230 5166 Planarity : 0.004 0.068 6186 Dihedral : 3.961 50.650 4804 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.07 % Favored : 96.86 % Rotamer: Outliers : 1.59 % Allowed : 10.29 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.13), residues: 4302 helix: 2.21 (0.10), residues: 2271 sheet: -0.30 (0.21), residues: 507 loop : -0.24 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 290 HIS 0.003 0.001 HIS B 303 PHE 0.019 0.001 PHE F 571 TYR 0.016 0.001 TYR E 50 ARG 0.006 0.000 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.03408 ( 1919) hydrogen bonds : angle 4.13418 ( 5592) covalent geometry : bond 0.00329 (34140) covalent geometry : angle 0.50675 (46356) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 139 time to evaluate : 3.838 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.7712 (m-70) cc_final: 0.7306 (m-70) REVERT: A 678 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8347 (tp30) REVERT: F 79 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8582 (pp) REVERT: F 218 PHE cc_start: 0.7213 (m-10) cc_final: 0.6784 (m-80) REVERT: F 225 ARG cc_start: 0.8331 (mmm-85) cc_final: 0.8052 (tpt90) REVERT: F 581 ASP cc_start: 0.8319 (p0) cc_final: 0.7698 (t0) REVERT: E 659 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7792 (pt0) REVERT: E 693 ARG cc_start: 0.7022 (OUTLIER) cc_final: 0.6655 (mmp-170) REVERT: E 711 GLU cc_start: 0.6542 (OUTLIER) cc_final: 0.6313 (mt-10) REVERT: D 79 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8275 (pp) REVERT: D 201 LEU cc_start: 0.8675 (tp) cc_final: 0.8414 (tp) REVERT: D 710 GLU cc_start: 0.7200 (tp30) cc_final: 0.6763 (tm-30) REVERT: C 205 TRP cc_start: 0.6603 (t60) cc_final: 0.6227 (t-100) REVERT: B 334 GLN cc_start: 0.7352 (OUTLIER) cc_final: 0.6987 (tt0) REVERT: B 484 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7346 (mp0) REVERT: B 708 ARG cc_start: 0.8064 (mmt-90) cc_final: 0.7834 (mmt-90) outliers start: 54 outliers final: 39 residues processed: 183 average time/residue: 0.4738 time to fit residues: 141.9540 Evaluate side-chains 173 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 127 time to evaluate : 3.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 209 TYR Chi-restraints excluded: chain F residue 246 ASP Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 433 MET Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 659 GLU Chi-restraints excluded: chain E residue 693 ARG Chi-restraints excluded: chain E residue 711 GLU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 566 THR Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 613 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 124 optimal weight: 6.9990 chunk 191 optimal weight: 10.0000 chunk 206 optimal weight: 0.9990 chunk 398 optimal weight: 0.9980 chunk 234 optimal weight: 4.9990 chunk 425 optimal weight: 7.9990 chunk 388 optimal weight: 6.9990 chunk 265 optimal weight: 6.9990 chunk 345 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.127805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.094106 restraints weight = 60551.515| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.62 r_work: 0.3245 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 34140 Z= 0.208 Angle : 0.561 12.890 46356 Z= 0.278 Chirality : 0.040 0.266 5166 Planarity : 0.004 0.066 6186 Dihedral : 4.086 51.869 4804 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.18 % Favored : 96.75 % Rotamer: Outliers : 1.70 % Allowed : 10.41 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.13), residues: 4302 helix: 2.07 (0.10), residues: 2271 sheet: -0.40 (0.21), residues: 501 loop : -0.28 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 290 HIS 0.006 0.001 HIS C 543 PHE 0.024 0.002 PHE B 218 TYR 0.018 0.002 TYR E 50 ARG 0.007 0.000 ARG D 298 Details of bonding type rmsd hydrogen bonds : bond 0.03596 ( 1919) hydrogen bonds : angle 4.23928 ( 5592) covalent geometry : bond 0.00490 (34140) covalent geometry : angle 0.56094 (46356) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 131 time to evaluate : 3.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.7713 (m-70) cc_final: 0.7322 (m-70) REVERT: F 80 TYR cc_start: 0.8921 (OUTLIER) cc_final: 0.8691 (m-80) REVERT: F 218 PHE cc_start: 0.7292 (m-10) cc_final: 0.6824 (m-80) REVERT: F 225 ARG cc_start: 0.8354 (mmm-85) cc_final: 0.8068 (tpt90) REVERT: F 581 ASP cc_start: 0.8305 (p0) cc_final: 0.7677 (t0) REVERT: E 659 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7800 (pt0) REVERT: E 693 ARG cc_start: 0.7181 (OUTLIER) cc_final: 0.6677 (mmp-170) REVERT: E 711 GLU cc_start: 0.6531 (OUTLIER) cc_final: 0.6239 (mt-10) REVERT: D 79 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8330 (pp) REVERT: D 201 LEU cc_start: 0.8659 (tp) cc_final: 0.8338 (tp) REVERT: D 710 GLU cc_start: 0.7192 (tp30) cc_final: 0.6704 (tm-30) REVERT: C 205 TRP cc_start: 0.6587 (t60) cc_final: 0.6227 (t-100) REVERT: B 334 GLN cc_start: 0.7358 (OUTLIER) cc_final: 0.6906 (tt0) REVERT: B 484 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7318 (mp0) REVERT: B 708 ARG cc_start: 0.7924 (mmt-90) cc_final: 0.7640 (mmt-90) outliers start: 58 outliers final: 43 residues processed: 180 average time/residue: 0.4689 time to fit residues: 138.0055 Evaluate side-chains 174 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 124 time to evaluate : 3.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 128 LYS Chi-restraints excluded: chain F residue 209 TYR Chi-restraints excluded: chain F residue 246 ASP Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 433 MET Chi-restraints excluded: chain F residue 578 ILE Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 703 LEU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 86 ARG Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 659 GLU Chi-restraints excluded: chain E residue 693 ARG Chi-restraints excluded: chain E residue 711 GLU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 566 THR Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 613 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 42 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 157 optimal weight: 20.0000 chunk 335 optimal weight: 5.9990 chunk 272 optimal weight: 1.9990 chunk 267 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 210 optimal weight: 2.9990 chunk 280 optimal weight: 3.9990 chunk 241 optimal weight: 2.9990 chunk 203 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 HIS ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.138735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.105016 restraints weight = 59963.754| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.65 r_work: 0.3272 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 34140 Z= 0.132 Angle : 0.511 12.871 46356 Z= 0.252 Chirality : 0.038 0.253 5166 Planarity : 0.004 0.069 6186 Dihedral : 3.963 50.683 4804 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.91 % Favored : 97.02 % Rotamer: Outliers : 1.65 % Allowed : 10.44 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.13), residues: 4302 helix: 2.23 (0.11), residues: 2271 sheet: -0.36 (0.21), residues: 507 loop : -0.23 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 205 HIS 0.003 0.001 HIS C 543 PHE 0.018 0.001 PHE B 218 TYR 0.015 0.001 TYR E 50 ARG 0.005 0.000 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.03392 ( 1919) hydrogen bonds : angle 4.10222 ( 5592) covalent geometry : bond 0.00305 (34140) covalent geometry : angle 0.51100 (46356) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 140 time to evaluate : 3.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.7683 (m-70) cc_final: 0.7302 (m-70) REVERT: A 678 GLU cc_start: 0.8420 (tp30) cc_final: 0.8069 (tp30) REVERT: A 689 MET cc_start: 0.7390 (mmm) cc_final: 0.7096 (mmm) REVERT: F 119 PHE cc_start: 0.7631 (m-80) cc_final: 0.7141 (m-80) REVERT: F 218 PHE cc_start: 0.7243 (m-10) cc_final: 0.6813 (m-80) REVERT: F 225 ARG cc_start: 0.8298 (mmm-85) cc_final: 0.8032 (tpt90) REVERT: E 659 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7766 (pt0) REVERT: E 693 ARG cc_start: 0.7130 (OUTLIER) cc_final: 0.6674 (mmp-170) REVERT: E 711 GLU cc_start: 0.6549 (OUTLIER) cc_final: 0.6283 (mt-10) REVERT: D 79 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8269 (pp) REVERT: D 201 LEU cc_start: 0.8677 (tp) cc_final: 0.8357 (tp) REVERT: D 578 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8164 (tt) REVERT: D 710 GLU cc_start: 0.7169 (tp30) cc_final: 0.6626 (tm-30) REVERT: C 205 TRP cc_start: 0.6535 (t60) cc_final: 0.6149 (t-100) REVERT: B 1 MET cc_start: 0.7279 (mtp) cc_final: 0.7059 (ptp) REVERT: B 484 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7332 (mp0) REVERT: B 708 ARG cc_start: 0.8037 (mmt-90) cc_final: 0.7835 (mmt-90) outliers start: 56 outliers final: 43 residues processed: 187 average time/residue: 0.4656 time to fit residues: 141.0964 Evaluate side-chains 181 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 132 time to evaluate : 3.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 128 LYS Chi-restraints excluded: chain F residue 209 TYR Chi-restraints excluded: chain F residue 246 ASP Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 578 ILE Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 703 LEU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 86 ARG Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 659 GLU Chi-restraints excluded: chain E residue 693 ARG Chi-restraints excluded: chain E residue 711 GLU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 566 THR Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 613 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 58 optimal weight: 7.9990 chunk 207 optimal weight: 7.9990 chunk 338 optimal weight: 2.9990 chunk 367 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 chunk 353 optimal weight: 7.9990 chunk 307 optimal weight: 10.0000 chunk 242 optimal weight: 0.1980 chunk 195 optimal weight: 5.9990 chunk 151 optimal weight: 8.9990 chunk 208 optimal weight: 0.8980 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 211 ASN ** E 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 HIS B 334 GLN ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.137996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.104212 restraints weight = 60102.467| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.63 r_work: 0.3259 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 34140 Z= 0.168 Angle : 0.532 12.692 46356 Z= 0.262 Chirality : 0.039 0.248 5166 Planarity : 0.004 0.067 6186 Dihedral : 3.989 51.167 4804 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.11 % Favored : 96.82 % Rotamer: Outliers : 1.62 % Allowed : 10.64 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.13), residues: 4302 helix: 2.19 (0.10), residues: 2271 sheet: -0.39 (0.21), residues: 507 loop : -0.23 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 290 HIS 0.005 0.001 HIS B 303 PHE 0.033 0.001 PHE B 218 TYR 0.017 0.002 TYR E 50 ARG 0.005 0.000 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.03461 ( 1919) hydrogen bonds : angle 4.14074 ( 5592) covalent geometry : bond 0.00394 (34140) covalent geometry : angle 0.53177 (46356) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17217.11 seconds wall clock time: 297 minutes 35.10 seconds (17855.10 seconds total)