Starting phenix.real_space_refine on Fri May 30 08:55:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k8z_36969/05_2025/8k8z_36969.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k8z_36969/05_2025/8k8z_36969.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k8z_36969/05_2025/8k8z_36969.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k8z_36969/05_2025/8k8z_36969.map" model { file = "/net/cci-nas-00/data/ceres_data/8k8z_36969/05_2025/8k8z_36969.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k8z_36969/05_2025/8k8z_36969.cif" } resolution = 2.83 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= 0.002 sd= 0.021 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 6282 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 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: 33486 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "F" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "E" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "D" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "C" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "B" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 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: 18.18, per 1000 atoms: 0.54 Number of scatterers: 33486 At special positions: 0 Unit cell: (128.74, 143.5, 174.66, 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 6282 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: 8.90 Conformation dependent library (CDL) restraints added in 4.6 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: 164 helices and 66 sheets defined 55.2% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.84 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 70 removed outlier: 3.516A pdb=" N THR A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 118 removed outlier: 4.033A pdb=" N VAL A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ASN A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 154 removed outlier: 3.704A pdb=" N LEU A 125 " --> pdb=" O GLN A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 221 removed outlier: 4.127A pdb=" N ASN A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG A 213 " --> pdb=" O TYR A 209 " (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 300 through 305 Processing helix chain 'A' and resid 314 through 320 Processing helix chain 'A' and resid 321 through 333 removed outlier: 4.650A pdb=" N ALA A 325 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 369 removed outlier: 3.502A pdb=" N PHE A 367 " --> pdb=" O THR A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 379 removed outlier: 3.809A pdb=" N SER A 377 " --> pdb=" O ASP A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 408 Processing helix chain 'A' and resid 412 through 428 Processing helix chain 'A' and resid 436 through 452 Processing helix chain 'A' and resid 456 through 471 removed outlier: 3.741A pdb=" N SER A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 531 through 535 Processing helix chain 'A' and resid 539 through 557 removed outlier: 3.830A pdb=" N LYS A 544 " --> pdb=" O GLN A 540 " (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: 4.637A pdb=" N ALA A 652 " --> pdb=" O ALA A 649 " (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 9 Processing helix chain 'F' and resid 32 through 46 Processing helix chain 'F' and resid 58 through 70 removed outlier: 3.524A pdb=" N THR F 69 " --> pdb=" O ALA F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 119 removed outlier: 4.025A pdb=" N VAL F 112 " --> pdb=" O LEU F 108 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ASN F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG F 114 " --> pdb=" O LEU F 110 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE F 119 " --> pdb=" O LEU F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 154 removed outlier: 3.699A pdb=" N LEU F 125 " --> pdb=" O GLN F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 221 removed outlier: 4.094A pdb=" N ASN F 212 " --> pdb=" O HIS F 208 " (cutoff:3.500A) removed outlier: 3.703A 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 242 Processing helix chain 'F' and resid 247 through 251 removed outlier: 3.907A pdb=" N ARG F 251 " --> pdb=" O ALA F 248 " (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 300 through 305 Processing helix chain 'F' and resid 314 through 320 Processing helix chain 'F' and resid 321 through 333 removed outlier: 4.622A pdb=" N ALA F 325 " --> pdb=" O GLY F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 369 removed outlier: 3.507A pdb=" N PHE F 367 " --> pdb=" O THR F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 379 removed outlier: 3.706A pdb=" N SER F 377 " --> pdb=" O ASP F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 407 Processing helix chain 'F' and resid 412 through 428 Processing helix chain 'F' and resid 436 through 452 Processing helix chain 'F' and resid 456 through 471 removed outlier: 3.729A 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 removed outlier: 3.796A pdb=" N LYS F 544 " --> pdb=" O GLN F 540 " (cutoff:3.500A) 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 654 removed outlier: 4.644A pdb=" N ALA F 652 " --> pdb=" O ALA F 649 " (cutoff:3.500A) 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 70 removed outlier: 3.526A pdb=" N THR E 69 " --> pdb=" O ALA E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 118 removed outlier: 4.035A pdb=" N VAL E 112 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ASN E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG E 114 " --> pdb=" O LEU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 154 removed outlier: 3.743A pdb=" N LEU E 125 " --> pdb=" O GLN E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 221 removed outlier: 4.116A pdb=" N ASN E 212 " --> pdb=" O HIS E 208 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG E 213 " --> pdb=" O TYR E 209 " (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 278 Processing helix chain 'E' and resid 293 through 295 No H-bonds generated for 'chain 'E' and resid 293 through 295' Processing helix chain 'E' and resid 300 through 305 Processing helix chain 'E' and resid 314 through 320 Processing helix chain 'E' and resid 321 through 333 removed outlier: 4.616A pdb=" N ALA E 325 " --> pdb=" O GLY E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 369 Processing helix chain 'E' and resid 373 through 379 removed outlier: 3.839A pdb=" N SER E 377 " --> pdb=" O ASP E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 408 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: 3.739A pdb=" N SER E 471 " --> pdb=" O ARG E 467 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'E' and resid 531 through 535 Processing helix chain 'E' and resid 539 through 557 removed outlier: 3.811A pdb=" N LYS E 544 " --> pdb=" O GLN E 540 " (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: 4.625A pdb=" N ALA E 652 " --> pdb=" O ALA E 649 " (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 70 removed outlier: 3.517A pdb=" N THR D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 118 removed outlier: 4.033A pdb=" N VAL D 112 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ASN D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG D 114 " --> pdb=" O LEU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 154 removed outlier: 3.705A pdb=" N LEU D 125 " --> pdb=" O GLN D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 221 removed outlier: 4.127A pdb=" N ASN D 212 " --> pdb=" O HIS D 208 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG D 213 " --> pdb=" O TYR D 209 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 224 through 242 Processing helix chain 'D' and resid 273 through 279 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 321 through 333 removed outlier: 4.656A pdb=" N ALA D 325 " --> pdb=" O GLY D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 369 removed outlier: 3.502A pdb=" N PHE D 367 " --> pdb=" O THR D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 379 removed outlier: 3.811A 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 428 Processing helix chain 'D' and resid 436 through 452 Processing helix chain 'D' and resid 456 through 471 removed outlier: 3.741A 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 removed outlier: 3.825A pdb=" N LYS D 544 " --> pdb=" O GLN D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 597 Processing helix chain 'D' and resid 621 through 637 Processing helix chain 'D' and resid 649 through 654 removed outlier: 4.636A pdb=" N ALA D 652 " --> pdb=" O ALA D 649 " (cutoff:3.500A) 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 70 removed outlier: 3.523A pdb=" N THR C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 119 removed outlier: 4.025A pdb=" N VAL C 112 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ASN C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE C 119 " --> pdb=" O LEU C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 154 removed outlier: 3.706A pdb=" N LEU C 125 " --> pdb=" O GLN C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 221 removed outlier: 4.094A pdb=" N ASN C 212 " --> pdb=" O HIS C 208 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG C 213 " --> pdb=" O TYR C 209 " (cutoff:3.500A) Proline residue: C 216 - end of helix Processing helix chain 'C' and resid 224 through 242 Processing helix chain 'C' and resid 247 through 251 removed outlier: 3.907A pdb=" N ARG C 251 " --> pdb=" O ALA C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 278 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 300 through 305 Processing helix chain 'C' and resid 314 through 320 Processing helix chain 'C' and resid 321 through 333 removed outlier: 4.617A pdb=" N ALA C 325 " --> pdb=" O GLY C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 369 removed outlier: 3.507A pdb=" N PHE C 367 " --> pdb=" O THR C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 379 removed outlier: 3.707A 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 428 Processing helix chain 'C' and resid 436 through 452 Processing helix chain 'C' and resid 456 through 471 removed outlier: 3.729A pdb=" N SER C 471 " --> pdb=" O ARG C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 484 Processing helix chain 'C' and resid 531 through 535 Processing helix chain 'C' and resid 539 through 557 removed outlier: 3.794A pdb=" N LYS C 544 " --> pdb=" O GLN C 540 " (cutoff:3.500A) 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: 4.648A pdb=" N ALA C 652 " --> pdb=" O ALA C 649 " (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 9 Processing helix chain 'B' and resid 32 through 46 Processing helix chain 'B' and resid 58 through 70 removed outlier: 3.525A pdb=" N THR B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 118 removed outlier: 4.038A pdb=" N VAL B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ASN B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 154 removed outlier: 3.683A pdb=" N LEU B 125 " --> pdb=" O GLN B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 221 removed outlier: 4.115A pdb=" N ASN B 212 " --> pdb=" O HIS B 208 " (cutoff:3.500A) removed outlier: 3.704A 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 242 Processing helix chain 'B' and resid 273 through 278 Processing helix chain 'B' and resid 293 through 295 No H-bonds generated for 'chain 'B' and resid 293 through 295' Processing helix chain 'B' and resid 300 through 305 Processing helix chain 'B' and resid 314 through 320 Processing helix chain 'B' and resid 321 through 333 removed outlier: 4.527A pdb=" N ALA B 325 " --> pdb=" O GLY B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 369 Processing helix chain 'B' and resid 373 through 379 removed outlier: 3.838A pdb=" N SER B 377 " --> pdb=" O ASP B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 408 Processing helix chain 'B' and resid 412 through 428 Processing helix chain 'B' and resid 436 through 452 Processing helix chain 'B' and resid 456 through 471 removed outlier: 3.739A 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 removed outlier: 3.812A pdb=" N LYS B 544 " --> pdb=" O GLN B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 597 Processing helix chain 'B' and resid 621 through 637 Processing helix chain 'B' and resid 649 through 654 removed outlier: 4.626A 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: 6.428A pdb=" N VAL A 267 " --> pdb=" O ILE A 311 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N ASP A 313 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N GLU A 269 " --> pdb=" O ASP A 313 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU A 310 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL A 361 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU A 312 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N HIS A 48 " --> pdb=" O PHE A 380 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE A 382 " --> pdb=" O HIS A 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 82 Processing sheet with id=AA3, first strand: chain 'A' and resid 156 through 158 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 285 Processing sheet with id=AA6, first strand: chain 'A' and resid 334 through 335 Processing sheet with id=AA7, first strand: chain 'A' and resid 389 through 391 Processing sheet with id=AA8, first strand: chain 'A' and resid 410 through 411 removed outlier: 7.026A pdb=" N GLN A 410 " --> pdb=" O LEU A 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 494 through 496 Processing sheet with id=AB1, first strand: chain 'A' and resid 528 through 530 removed outlier: 6.827A pdb=" N ILE A 529 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N PHE A 571 " --> pdb=" O ILE A 529 " (cutoff:3.500A) removed outlier: 9.727A pdb=" N GLU A 498 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N VAL A 606 " --> pdb=" O GLU A 498 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ASN A 500 " --> pdb=" O VAL A 606 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA A 605 " --> pdb=" O ILE A 645 " (cutoff:3.500A) 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: 6.446A pdb=" N VAL F 267 " --> pdb=" O ILE F 311 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N ASP F 313 " --> pdb=" O VAL F 267 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N GLU F 269 " --> pdb=" O ASP F 313 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU F 310 " --> pdb=" O ILE F 359 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL F 361 " --> pdb=" O LEU F 310 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU F 312 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N HIS F 48 " --> pdb=" O PHE F 380 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE F 382 " --> pdb=" O HIS F 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 77 through 82 Processing sheet with id=AB5, first strand: chain 'F' and resid 156 through 158 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 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: 7.003A 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 528 through 530 removed outlier: 6.806A pdb=" N ILE F 529 " --> pdb=" O LEU F 569 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N PHE F 571 " --> pdb=" O ILE F 529 " (cutoff:3.500A) removed outlier: 9.693A pdb=" N GLU F 498 " --> pdb=" O LEU F 604 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N VAL F 606 " --> pdb=" O GLU F 498 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ASN F 500 " --> pdb=" O VAL F 606 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA F 605 " --> pdb=" O ILE F 645 " (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 2 through 3 removed outlier: 4.739A pdb=" N ILE E 671 " --> pdb=" O LEU E 3 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA E 605 " --> pdb=" O ILE E 645 " (cutoff:3.500A) removed outlier: 9.682A pdb=" N GLU E 498 " --> pdb=" O LEU E 604 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N VAL E 606 " --> pdb=" O GLU E 498 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ASN E 500 " --> pdb=" O VAL E 606 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE E 529 " --> pdb=" O LEU E 569 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N PHE E 571 " --> pdb=" O ILE E 529 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 266 through 269 removed outlier: 6.431A pdb=" N VAL E 267 " --> pdb=" O ILE E 311 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N ASP E 313 " --> pdb=" O VAL E 267 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N GLU E 269 " --> pdb=" O ASP E 313 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU E 310 " --> pdb=" O ILE E 359 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL E 361 " --> pdb=" O LEU E 310 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU E 312 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N HIS E 48 " --> pdb=" O PHE E 380 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE E 382 " --> pdb=" O HIS E 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 77 through 82 Processing sheet with id=AC8, first strand: chain 'E' and resid 156 through 158 Processing sheet with id=AC9, first strand: chain 'E' and resid 280 through 281 Processing sheet with id=AD1, first strand: chain 'E' and resid 284 through 286 Processing sheet with id=AD2, first strand: chain 'E' and resid 334 through 335 Processing sheet with id=AD3, first strand: chain 'E' and resid 389 through 391 Processing sheet with id=AD4, first strand: chain 'E' and resid 410 through 411 removed outlier: 6.994A pdb=" N GLN E 410 " --> pdb=" O LEU E 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'E' and resid 494 through 496 Processing sheet with id=AD6, first strand: chain 'E' and resid 609 through 610 Processing sheet with id=AD7, first strand: chain 'D' and resid 266 through 269 removed outlier: 6.428A pdb=" N VAL D 267 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N ASP D 313 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N GLU D 269 " --> pdb=" O ASP D 313 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU D 310 " --> pdb=" O ILE D 359 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL D 361 " --> pdb=" O LEU D 310 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU D 312 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N HIS D 48 " --> pdb=" O PHE D 380 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE D 382 " --> pdb=" O HIS D 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 77 through 82 Processing sheet with id=AD9, first strand: chain 'D' and resid 156 through 158 Processing sheet with id=AE1, first strand: chain 'D' and resid 280 through 281 Processing sheet with id=AE2, first strand: chain 'D' and resid 284 through 285 Processing sheet with id=AE3, first strand: chain 'D' and resid 334 through 335 Processing sheet with id=AE4, first strand: chain 'D' and resid 389 through 391 Processing sheet with id=AE5, first strand: chain 'D' and resid 410 through 411 removed outlier: 7.025A pdb=" N GLN D 410 " --> pdb=" O LEU D 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'D' and resid 494 through 496 Processing sheet with id=AE7, first strand: chain 'D' and resid 528 through 530 removed outlier: 6.846A pdb=" N ILE D 529 " --> pdb=" O LEU D 569 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N PHE D 571 " --> pdb=" O ILE D 529 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N GLU D 498 " --> pdb=" O LEU D 604 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N VAL D 606 " --> pdb=" O GLU D 498 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ASN D 500 " --> pdb=" O VAL D 606 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA D 605 " --> pdb=" O ILE D 645 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 609 through 610 Processing sheet with id=AE9, first strand: chain 'C' and resid 266 through 269 removed outlier: 6.446A pdb=" N VAL C 267 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ASP C 313 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N GLU C 269 " --> pdb=" O ASP C 313 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU C 310 " --> pdb=" O ILE C 359 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL C 361 " --> pdb=" O LEU C 310 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU C 312 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N HIS C 48 " --> pdb=" O PHE C 380 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE C 382 " --> pdb=" O HIS C 48 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 77 through 82 Processing sheet with id=AF2, first strand: chain 'C' and resid 156 through 158 Processing sheet with id=AF3, first strand: chain 'C' and resid 280 through 281 Processing sheet with id=AF4, first strand: chain 'C' and resid 284 through 286 Processing sheet with id=AF5, first strand: chain 'C' and resid 334 through 335 Processing sheet with id=AF6, first strand: chain 'C' and resid 389 through 391 Processing sheet with id=AF7, first strand: chain 'C' and resid 410 through 411 removed outlier: 7.003A pdb=" N GLN C 410 " --> pdb=" O LEU C 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'C' and resid 494 through 496 Processing sheet with id=AF9, first strand: chain 'C' and resid 528 through 530 removed outlier: 6.800A pdb=" N ILE C 529 " --> pdb=" O LEU C 569 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N PHE C 571 " --> pdb=" O ILE C 529 " (cutoff:3.500A) removed outlier: 9.691A pdb=" N GLU C 498 " --> pdb=" O LEU C 604 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N VAL C 606 " --> pdb=" O GLU C 498 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ASN C 500 " --> pdb=" O VAL C 606 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA C 605 " --> pdb=" O ILE C 645 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 609 through 610 Processing sheet with id=AG2, first strand: chain 'B' and resid 2 through 3 removed outlier: 4.739A pdb=" N ILE B 671 " --> pdb=" O LEU B 3 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA B 605 " --> pdb=" O ILE B 645 " (cutoff:3.500A) removed outlier: 9.681A pdb=" N GLU B 498 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N VAL B 606 " --> pdb=" O GLU B 498 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASN B 500 " --> pdb=" O VAL B 606 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE B 529 " --> pdb=" O LEU B 569 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N PHE B 571 " --> pdb=" O ILE B 529 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 266 through 269 removed outlier: 6.432A pdb=" N VAL B 267 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ASP B 313 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N GLU B 269 " --> pdb=" O ASP B 313 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU B 310 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL B 361 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU B 312 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ALA B 49 " --> pdb=" O LEU B 360 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N GLY B 362 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU B 51 " --> pdb=" O GLY B 362 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N HIS B 48 " --> pdb=" O PHE B 380 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE B 382 " --> pdb=" O HIS B 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 77 through 82 Processing sheet with id=AG5, first strand: chain 'B' and resid 156 through 158 Processing sheet with id=AG6, first strand: chain 'B' and resid 280 through 281 Processing sheet with id=AG7, first strand: chain 'B' and resid 284 through 286 Processing sheet with id=AG8, first strand: chain 'B' and resid 334 through 335 Processing sheet with id=AG9, first strand: chain 'B' and resid 389 through 391 Processing sheet with id=AH1, first strand: chain 'B' and resid 410 through 411 removed outlier: 7.010A pdb=" N GLN B 410 " --> pdb=" O LEU B 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'B' and resid 494 through 496 Processing sheet with id=AH3, first strand: chain 'B' and resid 609 through 610 1924 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: 16.56 Time building geometry restraints manager: 10.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 11667 1.35 - 1.50: 8491 1.50 - 1.65: 13910 1.65 - 1.80: 48 1.80 - 1.94: 30 Bond restraints: 34146 Sorted by residual: bond pdb=" P TS6 F 801 " pdb=" S2P TS6 F 801 " ideal model delta sigma weight residual 2.275 1.943 0.332 2.00e-02 2.50e+03 2.76e+02 bond pdb=" P TS6 B 801 " pdb=" S2P TS6 B 801 " ideal model delta sigma weight residual 2.275 1.944 0.331 2.00e-02 2.50e+03 2.74e+02 bond pdb=" P TS6 D 801 " pdb=" S2P TS6 D 801 " ideal model delta sigma weight residual 2.275 1.944 0.331 2.00e-02 2.50e+03 2.74e+02 bond pdb=" P TS6 C 801 " pdb=" S2P TS6 C 801 " ideal model delta sigma weight residual 2.275 1.944 0.331 2.00e-02 2.50e+03 2.74e+02 bond pdb=" P TS6 A 801 " pdb=" S2P TS6 A 801 " ideal model delta sigma weight residual 2.275 1.944 0.331 2.00e-02 2.50e+03 2.74e+02 ... (remaining 34141 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 46111 3.41 - 6.83: 221 6.83 - 10.24: 6 10.24 - 13.66: 10 13.66 - 17.07: 14 Bond angle restraints: 46362 Sorted by residual: angle pdb=" O1P TS6 A 801 " pdb=" P TS6 A 801 " pdb=" S2P TS6 A 801 " ideal model delta sigma weight residual 98.15 115.22 -17.07 3.00e+00 1.11e-01 3.24e+01 angle pdb=" O1P TS6 B 801 " pdb=" P TS6 B 801 " pdb=" S2P TS6 B 801 " ideal model delta sigma weight residual 98.15 115.22 -17.07 3.00e+00 1.11e-01 3.24e+01 angle pdb=" O1P TS6 F 801 " pdb=" P TS6 F 801 " pdb=" S2P TS6 F 801 " ideal model delta sigma weight residual 98.15 115.21 -17.06 3.00e+00 1.11e-01 3.23e+01 angle pdb=" O1P TS6 E 801 " pdb=" P TS6 E 801 " pdb=" S2P TS6 E 801 " ideal model delta sigma weight residual 98.15 115.20 -17.05 3.00e+00 1.11e-01 3.23e+01 angle pdb=" O1P TS6 D 801 " pdb=" P TS6 D 801 " pdb=" S2P TS6 D 801 " ideal model delta sigma weight residual 98.15 115.13 -16.98 3.00e+00 1.11e-01 3.20e+01 ... (remaining 46357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.41: 18576 16.41 - 32.82: 1607 32.82 - 49.23: 341 49.23 - 65.65: 100 65.65 - 82.06: 100 Dihedral angle restraints: 20724 sinusoidal: 8394 harmonic: 12330 Sorted by residual: dihedral pdb=" CA GLN F 121 " pdb=" C GLN F 121 " pdb=" N GLY F 122 " pdb=" CA GLY F 122 " ideal model delta harmonic sigma weight residual -180.00 -162.30 -17.70 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA GLN E 121 " pdb=" C GLN E 121 " pdb=" N GLY E 122 " pdb=" CA GLY E 122 " ideal model delta harmonic sigma weight residual -180.00 -162.57 -17.43 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA GLN C 121 " pdb=" C GLN C 121 " pdb=" N GLY C 122 " pdb=" CA GLY C 122 " ideal model delta harmonic sigma weight residual -180.00 -162.57 -17.43 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 20721 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 4267 0.055 - 0.109: 730 0.109 - 0.164: 103 0.164 - 0.218: 48 0.218 - 0.273: 18 Chirality restraints: 5166 Sorted by residual: chirality pdb=" CA SER E 56 " pdb=" N SER E 56 " pdb=" C SER E 56 " pdb=" CB SER E 56 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA SER B 56 " pdb=" N SER B 56 " pdb=" C SER B 56 " pdb=" CB SER B 56 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA SER A 56 " pdb=" N SER A 56 " pdb=" C SER A 56 " pdb=" CB SER A 56 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 5163 not shown) Planarity restraints: 6186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 136 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.86e+00 pdb=" C LYS C 136 " 0.029 2.00e-02 2.50e+03 pdb=" O LYS C 136 " -0.011 2.00e-02 2.50e+03 pdb=" N GLU C 137 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 136 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.61e+00 pdb=" C LYS F 136 " 0.028 2.00e-02 2.50e+03 pdb=" O LYS F 136 " -0.010 2.00e-02 2.50e+03 pdb=" N GLU F 137 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 136 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.59e+00 pdb=" C LYS B 136 " 0.028 2.00e-02 2.50e+03 pdb=" O LYS B 136 " -0.010 2.00e-02 2.50e+03 pdb=" N GLU B 137 " -0.009 2.00e-02 2.50e+03 ... (remaining 6183 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1022 2.71 - 3.26: 34376 3.26 - 3.80: 58464 3.80 - 4.35: 72714 4.35 - 4.90: 122778 Nonbonded interactions: 289354 Sorted by model distance: nonbonded pdb=" NH1 ARG A 516 " pdb=" OE2 GLU A 572 " model vdw 2.160 3.120 nonbonded pdb=" OD2 ASP E 116 " pdb=" OH TYR E 238 " model vdw 2.198 3.040 nonbonded pdb=" OD2 ASP B 116 " pdb=" OH TYR B 238 " model vdw 2.201 3.040 nonbonded pdb=" OD2 ASP D 116 " pdb=" OH TYR D 238 " model vdw 2.203 3.040 nonbonded pdb=" OD2 ASP A 116 " pdb=" OH TYR A 238 " model vdw 2.204 3.040 ... (remaining 289349 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: 1.990 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: 1.280 Check model and map are aligned: 0.230 Set scattering table: 0.280 Process input model: 78.550 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.332 34146 Z= 0.353 Angle : 0.752 17.072 46362 Z= 0.427 Chirality : 0.047 0.273 5166 Planarity : 0.004 0.042 6186 Dihedral : 14.528 82.057 12804 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.29 % Allowed : 0.94 % Favored : 98.77 % 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: 1.30 (0.13), residues: 4302 helix: 1.50 (0.11), residues: 2274 sheet: -0.04 (0.23), residues: 546 loop : 0.39 (0.17), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 290 HIS 0.009 0.001 HIS B 543 PHE 0.018 0.001 PHE F 692 TYR 0.012 0.001 TYR F 420 ARG 0.008 0.000 ARG B 488 Details of bonding type rmsd hydrogen bonds : bond 0.14356 ( 1924) hydrogen bonds : angle 5.96215 ( 5592) covalent geometry : bond 0.00655 (34146) covalent geometry : angle 0.75227 (46362) *********************** 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 194 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 184 time to evaluate : 3.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 693 ARG cc_start: 0.7878 (mtm110) cc_final: 0.7482 (mtm-85) REVERT: D 342 GLN cc_start: 0.7707 (OUTLIER) cc_final: 0.7409 (pp30) REVERT: B 693 ARG cc_start: 0.7868 (mtm110) cc_final: 0.7483 (mtm-85) outliers start: 10 outliers final: 0 residues processed: 192 average time/residue: 1.8778 time to fit residues: 417.9920 Evaluate side-chains 97 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 3.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 342 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 359 optimal weight: 3.9990 chunk 322 optimal weight: 0.9990 chunk 179 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 217 optimal weight: 7.9990 chunk 172 optimal weight: 1.9990 chunk 333 optimal weight: 9.9990 chunk 129 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 386 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN ** A 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 332 ASN ** F 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 332 ASN ** E 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 332 ASN D 342 GLN ** D 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 ASN ** C 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** B 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.093676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.066891 restraints weight = 80500.128| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.86 r_work: 0.2788 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 34146 Z= 0.170 Angle : 0.587 9.939 46362 Z= 0.293 Chirality : 0.040 0.154 5166 Planarity : 0.004 0.044 6186 Dihedral : 4.123 34.490 4803 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.79 % Allowed : 6.48 % Favored : 92.72 % 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: 1.61 (0.11), residues: 2310 sheet: 0.05 (0.22), residues: 546 loop : 0.37 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 205 HIS 0.009 0.001 HIS E 543 PHE 0.013 0.001 PHE C 692 TYR 0.012 0.001 TYR A 50 ARG 0.008 0.000 ARG B 516 Details of bonding type rmsd hydrogen bonds : bond 0.04578 ( 1924) hydrogen bonds : angle 4.77643 ( 5592) covalent geometry : bond 0.00382 (34146) covalent geometry : angle 0.58715 (46362) *********************** 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 135 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 3.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 689 MET cc_start: 0.8717 (mtp) cc_final: 0.8495 (mmm) REVERT: B 689 MET cc_start: 0.8712 (mtp) cc_final: 0.8491 (mmm) outliers start: 27 outliers final: 6 residues processed: 127 average time/residue: 1.6416 time to fit residues: 248.9572 Evaluate side-chains 96 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 3.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain C residue 315 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 419 optimal weight: 5.9990 chunk 209 optimal weight: 4.9990 chunk 188 optimal weight: 5.9990 chunk 290 optimal weight: 0.9990 chunk 400 optimal weight: 2.9990 chunk 421 optimal weight: 6.9990 chunk 222 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 237 optimal weight: 0.6980 chunk 310 optimal weight: 7.9990 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 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 HIS ** F 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 560 HIS ** C 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 560 HIS ** B 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.083031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.056758 restraints weight = 81662.045| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.80 r_work: 0.2788 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 34146 Z= 0.148 Angle : 0.534 10.047 46362 Z= 0.267 Chirality : 0.039 0.163 5166 Planarity : 0.003 0.045 6186 Dihedral : 3.985 20.274 4800 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.06 % Allowed : 8.33 % Favored : 90.61 % 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: 1.52 (0.13), residues: 4302 helix: 1.73 (0.11), residues: 2304 sheet: 0.15 (0.22), residues: 546 loop : 0.32 (0.18), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 290 HIS 0.010 0.001 HIS E 543 PHE 0.014 0.001 PHE A 692 TYR 0.013 0.001 TYR A 50 ARG 0.005 0.000 ARG F 200 Details of bonding type rmsd hydrogen bonds : bond 0.04012 ( 1924) hydrogen bonds : angle 4.43200 ( 5592) covalent geometry : bond 0.00331 (34146) covalent geometry : angle 0.53406 (46362) *********************** 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 135 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 99 time to evaluate : 3.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 689 MET cc_start: 0.8708 (mtp) cc_final: 0.8435 (mmm) REVERT: B 689 MET cc_start: 0.8721 (mtp) cc_final: 0.8463 (mmm) REVERT: B 692 PHE cc_start: 0.8584 (t80) cc_final: 0.7593 (t80) REVERT: B 693 ARG cc_start: 0.8358 (ptm160) cc_final: 0.7726 (ptp90) outliers start: 36 outliers final: 17 residues processed: 127 average time/residue: 1.5915 time to fit residues: 241.6883 Evaluate side-chains 106 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 3.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 603 ASP Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 711 GLU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 716 GLU Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 285 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 59 optimal weight: 4.9990 chunk 377 optimal weight: 0.3980 chunk 3 optimal weight: 3.9990 chunk 216 optimal weight: 2.9990 chunk 368 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 151 optimal weight: 0.5980 chunk 401 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 336 optimal weight: 9.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 342 GLN ** F 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 560 HIS ** D 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 342 GLN ** C 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.082989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.056752 restraints weight = 81324.667| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.79 r_work: 0.2778 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 34146 Z= 0.147 Angle : 0.525 9.856 46362 Z= 0.260 Chirality : 0.039 0.162 5166 Planarity : 0.003 0.046 6186 Dihedral : 3.936 20.076 4800 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.20 % Allowed : 9.62 % Favored : 89.17 % 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: 1.64 (0.13), residues: 4302 helix: 1.76 (0.11), residues: 2352 sheet: 0.26 (0.22), residues: 546 loop : 0.45 (0.18), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 290 HIS 0.009 0.001 HIS E 543 PHE 0.017 0.001 PHE C 692 TYR 0.013 0.001 TYR A 50 ARG 0.004 0.000 ARG B 516 Details of bonding type rmsd hydrogen bonds : bond 0.03829 ( 1924) hydrogen bonds : angle 4.30944 ( 5592) covalent geometry : bond 0.00331 (34146) covalent geometry : angle 0.52544 (46362) *********************** 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 137 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 96 time to evaluate : 3.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 693 ARG cc_start: 0.8205 (mtm-85) cc_final: 0.7558 (ptp90) REVERT: E 689 MET cc_start: 0.8837 (mtp) cc_final: 0.8458 (mmm) REVERT: D 693 ARG cc_start: 0.8193 (mtm-85) cc_final: 0.7543 (ptp90) REVERT: B 689 MET cc_start: 0.8822 (mtp) cc_final: 0.8440 (mmm) REVERT: B 693 ARG cc_start: 0.8440 (ptm160) cc_final: 0.8204 (ptp90) outliers start: 41 outliers final: 23 residues processed: 127 average time/residue: 1.5164 time to fit residues: 231.9806 Evaluate side-chains 109 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 4.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 342 GLN Chi-restraints excluded: chain F residue 433 MET Chi-restraints excluded: chain F residue 716 GLU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 711 GLU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 342 GLN Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 646 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 121 optimal weight: 4.9990 chunk 266 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 410 optimal weight: 6.9990 chunk 206 optimal weight: 4.9990 chunk 264 optimal weight: 0.9990 chunk 203 optimal weight: 0.8980 chunk 388 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 243 optimal weight: 10.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.082807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.056567 restraints weight = 81186.620| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.78 r_work: 0.2771 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34146 Z= 0.154 Angle : 0.521 9.672 46362 Z= 0.258 Chirality : 0.038 0.163 5166 Planarity : 0.003 0.043 6186 Dihedral : 3.905 19.948 4800 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.00 % Allowed : 10.42 % Favored : 88.59 % 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: 1.73 (0.13), residues: 4302 helix: 1.84 (0.11), residues: 2346 sheet: 0.32 (0.22), residues: 546 loop : 0.46 (0.18), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 290 HIS 0.009 0.001 HIS B 543 PHE 0.017 0.001 PHE C 692 TYR 0.013 0.001 TYR D 50 ARG 0.004 0.000 ARG B 516 Details of bonding type rmsd hydrogen bonds : bond 0.03757 ( 1924) hydrogen bonds : angle 4.24152 ( 5592) covalent geometry : bond 0.00347 (34146) covalent geometry : angle 0.52058 (46362) *********************** 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 133 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 3.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 693 ARG cc_start: 0.8180 (mtm-85) cc_final: 0.7539 (ptp90) REVERT: F 141 GLN cc_start: 0.9477 (tm-30) cc_final: 0.9152 (tm-30) REVERT: E 689 MET cc_start: 0.8830 (mtp) cc_final: 0.8495 (mmm) REVERT: D 693 ARG cc_start: 0.8181 (mtm-85) cc_final: 0.7536 (ptp90) REVERT: C 141 GLN cc_start: 0.9481 (tm-30) cc_final: 0.9155 (tm-30) REVERT: B 689 MET cc_start: 0.8825 (mtp) cc_final: 0.8493 (mmm) outliers start: 34 outliers final: 25 residues processed: 126 average time/residue: 1.5031 time to fit residues: 228.9108 Evaluate side-chains 115 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 3.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 433 MET Chi-restraints excluded: chain F residue 603 ASP Chi-restraints excluded: chain F residue 716 GLU Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 711 GLU Chi-restraints excluded: chain D residue 716 GLU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 716 GLU Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 646 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 1 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 144 optimal weight: 0.8980 chunk 424 optimal weight: 4.9990 chunk 162 optimal weight: 10.0000 chunk 413 optimal weight: 4.9990 chunk 155 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 chunk 398 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 400 optimal weight: 0.7980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 342 GLN ** F 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 ASN C 342 GLN ** C 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.081691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.055001 restraints weight = 81299.395| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.81 r_work: 0.2751 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 34146 Z= 0.215 Angle : 0.548 9.530 46362 Z= 0.272 Chirality : 0.039 0.153 5166 Planarity : 0.003 0.041 6186 Dihedral : 3.953 20.178 4800 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.50 % Allowed : 10.56 % Favored : 87.94 % 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: 1.74 (0.13), residues: 4302 helix: 1.85 (0.11), residues: 2352 sheet: 0.33 (0.22), residues: 546 loop : 0.46 (0.18), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 290 HIS 0.010 0.001 HIS B 543 PHE 0.018 0.001 PHE C 692 TYR 0.014 0.001 TYR D 50 ARG 0.004 0.000 ARG B 516 Details of bonding type rmsd hydrogen bonds : bond 0.03846 ( 1924) hydrogen bonds : angle 4.24298 ( 5592) covalent geometry : bond 0.00493 (34146) covalent geometry : angle 0.54753 (46362) *********************** 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 143 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 92 time to evaluate : 3.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 141 GLN cc_start: 0.9487 (tm-30) cc_final: 0.9154 (tm-30) REVERT: E 689 MET cc_start: 0.8937 (mtp) cc_final: 0.8561 (mmm) REVERT: D 690 GLU cc_start: 0.8782 (mp0) cc_final: 0.8580 (pm20) REVERT: C 141 GLN cc_start: 0.9488 (tm-30) cc_final: 0.9155 (tm-30) REVERT: B 689 MET cc_start: 0.8933 (mtp) cc_final: 0.8562 (mmm) outliers start: 51 outliers final: 30 residues processed: 135 average time/residue: 1.4448 time to fit residues: 236.9857 Evaluate side-chains 120 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 4.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 433 MET Chi-restraints excluded: chain F residue 603 ASP Chi-restraints excluded: chain F residue 716 GLU Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 711 GLU Chi-restraints excluded: chain D residue 716 GLU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 716 GLU Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 646 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 269 optimal weight: 4.9990 chunk 333 optimal weight: 7.9990 chunk 363 optimal weight: 0.0770 chunk 362 optimal weight: 9.9990 chunk 130 optimal weight: 0.9990 chunk 356 optimal weight: 9.9990 chunk 209 optimal weight: 1.9990 chunk 310 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 235 optimal weight: 7.9990 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN F 342 GLN ** F 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 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 = 0.3464 r_free = 0.3464 target = 0.082444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.055873 restraints weight = 81046.647| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.81 r_work: 0.2765 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 34146 Z= 0.154 Angle : 0.525 9.750 46362 Z= 0.259 Chirality : 0.038 0.156 5166 Planarity : 0.003 0.041 6186 Dihedral : 3.920 20.012 4800 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.61 % Allowed : 10.68 % Favored : 87.71 % 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: 1.80 (0.13), residues: 4302 helix: 1.91 (0.11), residues: 2346 sheet: 0.37 (0.22), residues: 546 loop : 0.47 (0.18), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 290 HIS 0.009 0.001 HIS E 543 PHE 0.017 0.001 PHE C 692 TYR 0.013 0.001 TYR D 50 ARG 0.009 0.000 ARG C 200 Details of bonding type rmsd hydrogen bonds : bond 0.03700 ( 1924) hydrogen bonds : angle 4.16895 ( 5592) covalent geometry : bond 0.00349 (34146) covalent geometry : angle 0.52467 (46362) *********************** 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 154 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 99 time to evaluate : 3.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 692 PHE cc_start: 0.8431 (t80) cc_final: 0.7776 (t80) REVERT: F 141 GLN cc_start: 0.9497 (tm-30) cc_final: 0.9172 (tm-30) REVERT: F 342 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8514 (pp30) REVERT: E 689 MET cc_start: 0.8823 (mtp) cc_final: 0.8612 (mmm) REVERT: D 690 GLU cc_start: 0.8808 (mp0) cc_final: 0.8540 (pm20) REVERT: D 692 PHE cc_start: 0.8491 (t80) cc_final: 0.7786 (t80) REVERT: C 141 GLN cc_start: 0.9496 (tm-30) cc_final: 0.9172 (tm-30) REVERT: C 690 GLU cc_start: 0.8447 (mp0) cc_final: 0.8149 (pm20) REVERT: B 689 MET cc_start: 0.8817 (mtp) cc_final: 0.8613 (mmm) outliers start: 55 outliers final: 32 residues processed: 145 average time/residue: 1.4636 time to fit residues: 256.4571 Evaluate side-chains 121 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 88 time to evaluate : 3.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 342 GLN Chi-restraints excluded: chain F residue 433 MET Chi-restraints excluded: chain F residue 603 ASP Chi-restraints excluded: chain F residue 716 GLU Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 716 GLU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 716 GLU Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 646 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 158 optimal weight: 20.0000 chunk 22 optimal weight: 5.9990 chunk 254 optimal weight: 4.9990 chunk 353 optimal weight: 9.9990 chunk 339 optimal weight: 1.9990 chunk 335 optimal weight: 5.9990 chunk 396 optimal weight: 5.9990 chunk 230 optimal weight: 10.0000 chunk 124 optimal weight: 0.0970 chunk 25 optimal weight: 10.0000 chunk 312 optimal weight: 7.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN C 342 GLN ** C 543 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 = 0.3441 r_free = 0.3441 target = 0.081089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.054645 restraints weight = 81435.726| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.77 r_work: 0.2724 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 34146 Z= 0.266 Angle : 0.592 9.411 46362 Z= 0.294 Chirality : 0.040 0.151 5166 Planarity : 0.003 0.039 6186 Dihedral : 4.018 26.047 4800 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.56 % Allowed : 11.36 % Favored : 87.09 % 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: 1.80 (0.13), residues: 4302 helix: 1.89 (0.11), residues: 2352 sheet: 0.50 (0.22), residues: 534 loop : 0.42 (0.18), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 290 HIS 0.012 0.001 HIS D 543 PHE 0.019 0.001 PHE D 692 TYR 0.015 0.001 TYR A 50 ARG 0.009 0.000 ARG F 200 Details of bonding type rmsd hydrogen bonds : bond 0.03890 ( 1924) hydrogen bonds : angle 4.24597 ( 5592) covalent geometry : bond 0.00608 (34146) covalent geometry : angle 0.59156 (46362) *********************** 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 152 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 99 time to evaluate : 3.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 141 GLN cc_start: 0.9495 (tm-30) cc_final: 0.9167 (tm-30) REVERT: F 690 GLU cc_start: 0.8227 (pm20) cc_final: 0.7885 (pm20) REVERT: E 689 MET cc_start: 0.8900 (mtp) cc_final: 0.8654 (mmm) REVERT: D 690 GLU cc_start: 0.8798 (mp0) cc_final: 0.8468 (pm20) REVERT: C 141 GLN cc_start: 0.9497 (tm-30) cc_final: 0.9172 (tm-30) REVERT: C 342 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8447 (pp30) REVERT: C 690 GLU cc_start: 0.8465 (mp0) cc_final: 0.8134 (pm20) REVERT: B 689 MET cc_start: 0.8891 (mtp) cc_final: 0.8626 (mmm) outliers start: 53 outliers final: 31 residues processed: 141 average time/residue: 1.5217 time to fit residues: 257.1505 Evaluate side-chains 123 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 91 time to evaluate : 3.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 603 ASP Chi-restraints excluded: chain F residue 716 GLU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 716 GLU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 342 GLN Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 716 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 716 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 341 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 367 optimal weight: 0.9980 chunk 294 optimal weight: 0.8980 chunk 416 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 381 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 chunk 405 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 GLN ** F 543 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 = 0.3459 r_free = 0.3459 target = 0.082234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.055694 restraints weight = 80641.405| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.79 r_work: 0.2760 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34146 Z= 0.150 Angle : 0.553 9.638 46362 Z= 0.273 Chirality : 0.038 0.155 5166 Planarity : 0.003 0.038 6186 Dihedral : 3.996 25.922 4800 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.38 % Allowed : 11.71 % Favored : 86.91 % 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: 1.83 (0.13), residues: 4302 helix: 1.94 (0.11), residues: 2346 sheet: 0.34 (0.22), residues: 546 loop : 0.48 (0.18), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 290 HIS 0.008 0.001 HIS A 543 PHE 0.021 0.001 PHE D 692 TYR 0.013 0.001 TYR D 50 ARG 0.009 0.000 ARG F 200 Details of bonding type rmsd hydrogen bonds : bond 0.03711 ( 1924) hydrogen bonds : angle 4.16164 ( 5592) covalent geometry : bond 0.00341 (34146) covalent geometry : angle 0.55273 (46362) *********************** 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 148 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 101 time to evaluate : 4.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 141 GLN cc_start: 0.9500 (tm-30) cc_final: 0.9175 (tm-30) REVERT: F 690 GLU cc_start: 0.8257 (pm20) cc_final: 0.7888 (pm20) REVERT: E 689 MET cc_start: 0.8829 (mtp) cc_final: 0.8341 (mmm) REVERT: D 690 GLU cc_start: 0.8789 (mp0) cc_final: 0.8514 (pm20) REVERT: C 141 GLN cc_start: 0.9501 (tm-30) cc_final: 0.9178 (tm-30) REVERT: B 689 MET cc_start: 0.8823 (mtp) cc_final: 0.8340 (mmm) outliers start: 47 outliers final: 30 residues processed: 140 average time/residue: 1.5076 time to fit residues: 255.3075 Evaluate side-chains 122 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 4.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 603 ASP Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 716 GLU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 716 GLU Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 716 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 70 optimal weight: 5.9990 chunk 9 optimal weight: 0.3980 chunk 221 optimal weight: 0.0870 chunk 287 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 361 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 245 optimal weight: 3.9990 chunk 96 optimal weight: 0.0570 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 160 ASN ** F 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.083552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.057543 restraints weight = 80833.314| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.78 r_work: 0.2797 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 34146 Z= 0.109 Angle : 0.546 9.622 46362 Z= 0.271 Chirality : 0.038 0.156 5166 Planarity : 0.003 0.042 6186 Dihedral : 3.949 25.395 4800 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.94 % Allowed : 12.18 % Favored : 86.88 % 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: 1.87 (0.13), residues: 4302 helix: 1.98 (0.11), residues: 2346 sheet: 0.38 (0.22), residues: 546 loop : 0.48 (0.18), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 290 HIS 0.006 0.001 HIS B 543 PHE 0.019 0.001 PHE D 692 TYR 0.011 0.001 TYR C 420 ARG 0.011 0.000 ARG E 688 Details of bonding type rmsd hydrogen bonds : bond 0.03517 ( 1924) hydrogen bonds : angle 4.07190 ( 5592) covalent geometry : bond 0.00243 (34146) covalent geometry : angle 0.54632 (46362) ********************** 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 138 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 106 time to evaluate : 3.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 141 GLN cc_start: 0.9506 (tm-30) cc_final: 0.9178 (tm-30) REVERT: F 690 GLU cc_start: 0.8262 (pm20) cc_final: 0.7937 (pm20) REVERT: D 690 GLU cc_start: 0.8768 (mp0) cc_final: 0.8513 (pm20) REVERT: C 141 GLN cc_start: 0.9509 (tm-30) cc_final: 0.9193 (tm-30) REVERT: B 693 ARG cc_start: 0.8460 (ptp-170) cc_final: 0.8124 (ptp90) outliers start: 32 outliers final: 24 residues processed: 133 average time/residue: 1.5317 time to fit residues: 245.5707 Evaluate side-chains 115 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 3.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 603 ASP Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 716 GLU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 716 GLU Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 716 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 299 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 93 optimal weight: 0.5980 chunk 349 optimal weight: 2.9990 chunk 343 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 165 optimal weight: 9.9990 chunk 270 optimal weight: 8.9990 chunk 244 optimal weight: 0.8980 chunk 373 optimal weight: 0.3980 chunk 77 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.083544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.057911 restraints weight = 81263.313| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.83 r_work: 0.2807 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34146 Z= 0.114 Angle : 0.540 9.373 46362 Z= 0.268 Chirality : 0.038 0.154 5166 Planarity : 0.003 0.039 6186 Dihedral : 3.882 25.753 4800 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.85 % Allowed : 12.41 % Favored : 86.74 % 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: 1.95 (0.13), residues: 4302 helix: 2.02 (0.11), residues: 2346 sheet: 0.45 (0.23), residues: 546 loop : 0.54 (0.18), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 290 HIS 0.007 0.001 HIS A 543 PHE 0.021 0.001 PHE D 692 TYR 0.011 0.001 TYR D 420 ARG 0.008 0.000 ARG F 200 Details of bonding type rmsd hydrogen bonds : bond 0.03479 ( 1924) hydrogen bonds : angle 4.02103 ( 5592) covalent geometry : bond 0.00255 (34146) covalent geometry : angle 0.53950 (46362) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16335.38 seconds wall clock time: 282 minutes 48.10 seconds (16968.10 seconds total)