Starting phenix.real_space_refine on Sat Jun 28 17:36:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k8z_36969/06_2025/8k8z_36969.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k8z_36969/06_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_36969/06_2025/8k8z_36969.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k8z_36969/06_2025/8k8z_36969.map" model { file = "/net/cci-nas-00/data/ceres_data/8k8z_36969/06_2025/8k8z_36969.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k8z_36969/06_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): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 19.79, per 1000 atoms: 0.59 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: 8.38 Conformation dependent library (CDL) restraints added in 4.5 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: 4.59 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: 15.87 Time building geometry restraints manager: 9.97 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: 2.040 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: 0.060 Extract box with map and model: 1.430 Check model and map are aligned: 0.260 Set scattering table: 0.280 Process input model: 79.370 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.800 ------------------------------------------------------------------------------- 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 : 3.529 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: 1.9399 time to fit residues: 430.3025 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 : 3.510 ------------------------------------------------------------------------------- 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 = 47)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.066872 restraints weight = 80500.129| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.87 r_work: 0.2791 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 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 : 3.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 689 MET cc_start: 0.8709 (mtp) cc_final: 0.8485 (mmm) REVERT: B 689 MET cc_start: 0.8704 (mtp) cc_final: 0.8481 (mmm) outliers start: 27 outliers final: 6 residues processed: 127 average time/residue: 1.6985 time to fit residues: 256.9751 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 : 3.653 ------------------------------------------------------------------------------- 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: 0.6980 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: 3.9990 chunk 237 optimal weight: 0.9980 chunk 310 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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** ** B 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 = 0.3479 r_free = 0.3479 target = 0.083268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.057474 restraints weight = 81394.693| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.79 r_work: 0.2796 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 34146 Z= 0.137 Angle : 0.530 10.054 46362 Z= 0.265 Chirality : 0.039 0.166 5166 Planarity : 0.003 0.049 6186 Dihedral : 3.977 20.284 4800 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.03 % Allowed : 8.33 % Favored : 90.64 % 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: 1.51 (0.13), residues: 4302 helix: 1.72 (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 0.009 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 0.04007 ( 1924) hydrogen bonds : angle 4.43158 ( 5592) covalent geometry : bond 0.00305 (34146) covalent geometry : angle 0.53031 (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 137 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 102 time to evaluate : 3.657 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: 0.8722 (mtp) cc_final: 0.8461 (mmm) REVERT: B 689 MET cc_start: 0.8716 (mtp) cc_final: 0.8465 (mmm) REVERT: B 692 PHE cc_start: 0.8587 (t80) cc_final: 0.7594 (t80) REVERT: B 693 ARG cc_start: 0.8355 (ptm160) cc_final: 0.7722 (ptp90) outliers start: 35 outliers final: 17 residues processed: 130 average time/residue: 1.6734 time to fit residues: 260.6504 Evaluate side-chains 105 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 3.623 ------------------------------------------------------------------------------- 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: 0.0980 chunk 377 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 216 optimal weight: 2.9990 chunk 368 optimal weight: 9.9990 chunk 1 optimal weight: 0.5980 chunk 196 optimal weight: 0.8980 chunk 151 optimal weight: 0.0570 chunk 401 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 336 optimal weight: 8.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- 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** C 342 GLN ** C 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 = 0.3505 r_free = 0.3505 target = 0.084535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.058640 restraints weight = 81082.155| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.79 r_work: 0.2824 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 34146 Z= 0.102 Angle : 0.508 9.761 46362 Z= 0.251 Chirality : 0.038 0.175 5166 Planarity : 0.003 0.053 6186 Dihedral : 3.869 19.692 4800 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.91 % Allowed : 9.57 % Favored : 89.52 % 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: 1.69 (0.13), residues: 4302 helix: 1.86 (0.11), residues: 2310 sheet: 0.29 (0.22), residues: 546 loop : 0.39 (0.18), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 290 HIS 0.007 0.000 HIS B 543 PHE 0.016 0.001 PHE C 692 TYR 0.011 0.001 TYR D 50 ARG 0.003 0.000 ARG C 200 Details of bonding type rmsd hydrogen bonds : bond 0.03655 ( 1924) hydrogen bonds : angle 4.22868 ( 5592) covalent geometry : bond 0.00216 (34146) covalent geometry : angle 0.50848 (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 136 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 105 time to evaluate : 3.449 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: 0.8548 (t80) cc_final: 0.7670 (t80) REVERT: F 141 GLN cc_start: 0.9478 (tm-30) cc_final: 0.9154 (tm-30) REVERT: E 365 GLU cc_start: 0.8714 (mp0) cc_final: 0.8322 (pm20) REVERT: E 689 MET cc_start: 0.8780 (mtp) cc_final: 0.8287 (mmm) REVERT: D 692 PHE cc_start: 0.8536 (t80) cc_final: 0.7659 (t80) REVERT: B 689 MET cc_start: 0.8766 (mtp) cc_final: 0.8275 (mmm) REVERT: B 693 ARG cc_start: 0.8414 (ptm160) cc_final: 0.8160 (ptp90) outliers start: 31 outliers final: 16 residues processed: 133 average time/residue: 1.5406 time to fit residues: 247.4797 Evaluate side-chains 107 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 4.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 GLU 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 716 GLU Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain D residue 140 GLU 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 342 GLN 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: 5.9990 chunk 266 optimal weight: 8.9990 chunk 67 optimal weight: 0.0040 chunk 129 optimal weight: 2.9990 chunk 410 optimal weight: 6.9990 chunk 206 optimal weight: 5.9990 chunk 264 optimal weight: 2.9990 chunk 203 optimal weight: 0.9990 chunk 388 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 243 optimal weight: 0.9980 overall best weight: 1.5998 ------------------------------------------------------------------------------- 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** ** D 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 342 GLN ** C 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 560 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.083484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.057325 restraints weight = 80887.206| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.79 r_work: 0.2798 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 34146 Z= 0.143 Angle : 0.510 9.704 46362 Z= 0.252 Chirality : 0.038 0.157 5166 Planarity : 0.003 0.045 6186 Dihedral : 3.827 20.066 4800 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.23 % Allowed : 10.09 % Favored : 88.67 % 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: 1.81 (0.13), residues: 4302 helix: 1.90 (0.11), residues: 2346 sheet: 0.40 (0.22), residues: 546 loop : 0.49 (0.18), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 290 HIS 0.008 0.001 HIS E 543 PHE 0.017 0.001 PHE C 692 TYR 0.013 0.001 TYR F 557 ARG 0.005 0.000 ARG D 693 Details of bonding type rmsd hydrogen bonds : bond 0.03648 ( 1924) hydrogen bonds : angle 4.17193 ( 5592) covalent geometry : bond 0.00322 (34146) covalent geometry : angle 0.51007 (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 143 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 101 time to evaluate : 3.541 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: E 689 MET cc_start: 0.8749 (mtp) cc_final: 0.8455 (mmm) REVERT: C 141 GLN cc_start: 0.9492 (tm-30) cc_final: 0.9173 (tm-30) REVERT: B 689 MET cc_start: 0.8748 (mtp) cc_final: 0.8468 (mmm) outliers start: 42 outliers final: 26 residues processed: 133 average time/residue: 1.5209 time to fit residues: 244.9737 Evaluate side-chains 114 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 88 time to evaluate : 3.790 ------------------------------------------------------------------------------- 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 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 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 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 118 LEU Chi-restraints excluded: chain B residue 140 GLU 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: 0.8980 chunk 89 optimal weight: 20.0000 chunk 144 optimal weight: 0.9990 chunk 424 optimal weight: 1.9990 chunk 162 optimal weight: 10.0000 chunk 413 optimal weight: 4.9990 chunk 155 optimal weight: 8.9990 chunk 131 optimal weight: 2.9990 chunk 398 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 400 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN ** 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 160 ASN ** C 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.082679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.056442 restraints weight = 81539.771| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.80 r_work: 0.2773 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 34146 Z= 0.173 Angle : 0.531 9.645 46362 Z= 0.264 Chirality : 0.039 0.154 5166 Planarity : 0.003 0.040 6186 Dihedral : 3.858 20.038 4800 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.50 % Allowed : 10.33 % Favored : 88.17 % 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: 1.88 (0.13), residues: 4302 helix: 1.94 (0.11), residues: 2346 sheet: 0.60 (0.22), residues: 534 loop : 0.48 (0.18), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 290 HIS 0.010 0.001 HIS E 543 PHE 0.018 0.001 PHE C 692 TYR 0.014 0.001 TYR F 557 ARG 0.004 0.000 ARG B 516 Details of bonding type rmsd hydrogen bonds : bond 0.03683 ( 1924) hydrogen bonds : angle 4.15750 ( 5592) covalent geometry : bond 0.00391 (34146) covalent geometry : angle 0.53078 (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 149 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 98 time to evaluate : 3.803 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: E 689 MET cc_start: 0.8875 (mtp) cc_final: 0.8564 (mmm) REVERT: B 689 MET cc_start: 0.8875 (mtp) cc_final: 0.8577 (mmm) outliers start: 51 outliers final: 31 residues processed: 136 average time/residue: 1.3899 time to fit residues: 230.3300 Evaluate side-chains 120 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 89 time to evaluate : 3.569 ------------------------------------------------------------------------------- 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 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 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 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: 10.0000 chunk 333 optimal weight: 9.9990 chunk 363 optimal weight: 0.0020 chunk 362 optimal weight: 8.9990 chunk 130 optimal weight: 0.6980 chunk 356 optimal weight: 6.9990 chunk 209 optimal weight: 3.9990 chunk 310 optimal weight: 4.9990 chunk 73 optimal weight: 0.3980 chunk 28 optimal weight: 4.9990 chunk 235 optimal weight: 6.9990 overall best weight: 2.0192 ------------------------------------------------------------------------------- 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** ** C 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 = 0.3469 r_free = 0.3469 target = 0.082569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.056348 restraints weight = 81586.450| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.79 r_work: 0.2770 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 34146 Z= 0.164 Angle : 0.531 9.709 46362 Z= 0.263 Chirality : 0.039 0.154 5166 Planarity : 0.003 0.041 6186 Dihedral : 3.863 19.703 4800 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.47 % Allowed : 10.86 % Favored : 87.68 % 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: 1.89 (0.13), residues: 4302 helix: 1.96 (0.11), residues: 2346 sheet: 0.44 (0.22), residues: 546 loop : 0.52 (0.18), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 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 A 50 ARG 0.008 0.000 ARG C 200 Details of bonding type rmsd hydrogen bonds : bond 0.03661 ( 1924) hydrogen bonds : angle 4.13303 ( 5592) covalent geometry : bond 0.00373 (34146) covalent geometry : angle 0.53063 (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 145 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 95 time to evaluate : 3.812 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: E 689 MET cc_start: 0.8867 (mtp) cc_final: 0.8330 (mmm) REVERT: B 689 MET cc_start: 0.8855 (mtp) cc_final: 0.8337 (mmm) outliers start: 50 outliers final: 29 residues processed: 136 average time/residue: 1.3778 time to fit residues: 229.8969 Evaluate side-chains 115 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 86 time to evaluate : 3.523 ------------------------------------------------------------------------------- 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 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 646 LEU Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 183 VAL 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 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: 4.9990 chunk 254 optimal weight: 2.9990 chunk 353 optimal weight: 9.9990 chunk 339 optimal weight: 0.4980 chunk 335 optimal weight: 3.9990 chunk 396 optimal weight: 3.9990 chunk 230 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 312 optimal weight: 6.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 160 ASN F 342 GLN ** F 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN C 160 ASN ** C 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.081916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.055603 restraints weight = 81356.751| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.78 r_work: 0.2749 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 34146 Z= 0.212 Angle : 0.563 9.529 46362 Z= 0.279 Chirality : 0.039 0.152 5166 Planarity : 0.003 0.041 6186 Dihedral : 3.915 24.959 4800 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.61 % Allowed : 11.30 % 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: 1.91 (0.13), residues: 4302 helix: 1.96 (0.11), residues: 2346 sheet: 0.56 (0.23), residues: 534 loop : 0.50 (0.18), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 290 HIS 0.010 0.001 HIS A 543 PHE 0.020 0.001 PHE D 692 TYR 0.014 0.001 TYR F 557 ARG 0.009 0.000 ARG F 200 Details of bonding type rmsd hydrogen bonds : bond 0.03752 ( 1924) hydrogen bonds : angle 4.16306 ( 5592) covalent geometry : bond 0.00485 (34146) covalent geometry : angle 0.56270 (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 146 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 91 time to evaluate : 3.834 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: E 200 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8560 (tpt90) REVERT: E 689 MET cc_start: 0.8663 (mtp) cc_final: 0.8173 (mmm) REVERT: C 689 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.8169 (mtm) REVERT: C 690 GLU cc_start: 0.8452 (mp0) cc_final: 0.8199 (pm20) REVERT: B 200 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8572 (tpt90) REVERT: B 356 MET cc_start: 0.9273 (OUTLIER) cc_final: 0.7935 (ppp) REVERT: B 689 MET cc_start: 0.8649 (mtp) cc_final: 0.8172 (mmm) outliers start: 55 outliers final: 35 residues processed: 131 average time/residue: 1.5622 time to fit residues: 246.4899 Evaluate side-chains 128 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 89 time to evaluate : 3.768 ------------------------------------------------------------------------------- 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 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 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 200 ARG 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 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 315 LEU Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 689 MET 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 200 ARG Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 438 VAL 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: 0.9990 chunk 149 optimal weight: 3.9990 chunk 217 optimal weight: 2.9990 chunk 367 optimal weight: 5.9990 chunk 294 optimal weight: 6.9990 chunk 416 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 381 optimal weight: 0.9990 chunk 114 optimal weight: 0.3980 chunk 171 optimal weight: 9.9990 chunk 405 optimal weight: 2.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 GLN F 342 GLN ** F 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN ** C 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.082523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.055989 restraints weight = 80805.608| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.81 r_work: 0.2768 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1766 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= 0.149 Angle : 0.539 9.646 46362 Z= 0.266 Chirality : 0.038 0.155 5166 Planarity : 0.003 0.042 6186 Dihedral : 3.892 25.102 4800 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.23 % Allowed : 11.88 % 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: 1.90 (0.13), residues: 4302 helix: 1.97 (0.11), residues: 2346 sheet: 0.43 (0.23), residues: 546 loop : 0.53 (0.18), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP F 290 HIS 0.008 0.001 HIS B 543 PHE 0.020 0.001 PHE D 692 TYR 0.013 0.001 TYR A 50 ARG 0.009 0.000 ARG F 200 Details of bonding type rmsd hydrogen bonds : bond 0.03638 ( 1924) hydrogen bonds : angle 4.10080 ( 5592) covalent geometry : bond 0.00338 (34146) covalent geometry : angle 0.53862 (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 135 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 93 time to evaluate : 3.724 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: F 141 GLN cc_start: 0.9508 (tm-30) cc_final: 0.9190 (tm-30) REVERT: F 690 GLU cc_start: 0.8194 (pm20) cc_final: 0.7817 (pm20) REVERT: E 200 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8555 (tpt90) REVERT: E 689 MET cc_start: 0.8631 (mtp) cc_final: 0.8065 (mmm) REVERT: E 690 GLU cc_start: 0.8336 (pm20) cc_final: 0.8022 (pp20) REVERT: C 690 GLU cc_start: 0.8511 (mp0) cc_final: 0.8256 (pm20) REVERT: B 200 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8567 (tpt90) REVERT: B 689 MET cc_start: 0.8603 (mtp) cc_final: 0.8025 (mmm) REVERT: B 690 GLU cc_start: 0.8359 (pm20) cc_final: 0.8048 (pp20) outliers start: 42 outliers final: 29 residues processed: 127 average time/residue: 1.5129 time to fit residues: 232.6722 Evaluate side-chains 122 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 91 time to evaluate : 3.616 ------------------------------------------------------------------------------- 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 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 200 ARG 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 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 200 ARG Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 438 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: 7.9990 chunk 9 optimal weight: 0.9980 chunk 221 optimal weight: 0.0050 chunk 287 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 125 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 361 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 245 optimal weight: 0.9980 chunk 96 optimal weight: 0.0470 overall best weight: 0.5492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 342 GLN F 540 GLN ** F 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 = 0.3501 r_free = 0.3501 target = 0.084138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.058293 restraints weight = 80999.951| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.79 r_work: 0.2820 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 34146 Z= 0.103 Angle : 0.517 9.618 46362 Z= 0.256 Chirality : 0.038 0.157 5166 Planarity : 0.003 0.043 6186 Dihedral : 3.822 25.808 4800 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.03 % Allowed : 12.21 % Favored : 86.77 % 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: 1.95 (0.13), residues: 4302 helix: 2.00 (0.11), residues: 2352 sheet: 0.50 (0.23), residues: 546 loop : 0.54 (0.18), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 290 HIS 0.006 0.001 HIS B 543 PHE 0.018 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 0.03432 ( 1924) hydrogen bonds : angle 3.99062 ( 5592) covalent geometry : bond 0.00226 (34146) covalent geometry : angle 0.51673 (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 153 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 118 time to evaluate : 4.076 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: 0.9182 (tm-30) REVERT: F 690 GLU cc_start: 0.8205 (pm20) cc_final: 0.7859 (pm20) REVERT: E 200 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8519 (tpt90) REVERT: E 365 GLU cc_start: 0.8679 (mp0) cc_final: 0.8220 (pm20) REVERT: E 690 GLU cc_start: 0.8334 (pm20) cc_final: 0.8062 (pp20) REVERT: C 690 GLU cc_start: 0.8461 (mp0) cc_final: 0.8202 (pm20) REVERT: B 200 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8548 (tpt90) REVERT: B 690 GLU cc_start: 0.8376 (pm20) cc_final: 0.8089 (pp20) REVERT: B 693 ARG cc_start: 0.8487 (ptp-170) cc_final: 0.8137 (ptp90) outliers start: 35 outliers final: 27 residues processed: 147 average time/residue: 1.7952 time to fit residues: 320.0688 Evaluate side-chains 137 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 5.165 ------------------------------------------------------------------------------- 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 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 200 ARG 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 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 200 ARG Chi-restraints excluded: chain B residue 438 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 299 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 349 optimal weight: 2.9990 chunk 343 optimal weight: 0.0970 chunk 99 optimal weight: 1.9990 chunk 165 optimal weight: 10.0000 chunk 270 optimal weight: 8.9990 chunk 244 optimal weight: 4.9990 chunk 373 optimal weight: 0.0570 chunk 77 optimal weight: 4.9990 overall best weight: 1.8302 ------------------------------------------------------------------------------- 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** ** 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 = 0.3471 r_free = 0.3471 target = 0.082818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.056366 restraints weight = 81212.698| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.83 r_work: 0.2779 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 34146 Z= 0.157 Angle : 0.541 9.076 46362 Z= 0.268 Chirality : 0.038 0.153 5166 Planarity : 0.003 0.041 6186 Dihedral : 3.821 24.771 4800 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.91 % Allowed : 12.76 % Favored : 86.33 % 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: 2.03 (0.13), residues: 4302 helix: 2.03 (0.11), residues: 2352 sheet: 0.65 (0.23), residues: 534 loop : 0.60 (0.18), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 290 HIS 0.009 0.001 HIS D 543 PHE 0.018 0.001 PHE C 692 TYR 0.014 0.001 TYR E 557 ARG 0.009 0.000 ARG A 516 Details of bonding type rmsd hydrogen bonds : bond 0.03536 ( 1924) hydrogen bonds : angle 4.02857 ( 5592) covalent geometry : bond 0.00358 (34146) covalent geometry : angle 0.54116 (46362) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17540.29 seconds wall clock time: 300 minutes 5.42 seconds (18005.42 seconds total)