Starting phenix.real_space_refine on Tue Aug 26 04:26:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k8z_36969/08_2025/8k8z_36969.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k8z_36969/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8k8z_36969/08_2025/8k8z_36969.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k8z_36969/08_2025/8k8z_36969.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k8z_36969/08_2025/8k8z_36969.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k8z_36969/08_2025/8k8z_36969.map" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 7.72, per 1000 atoms: 0.23 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: 2.92 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.32 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: 7.44 Time building geometry restraints manager: 3.75 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: 0.02 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: 3.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 30.770 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.960 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (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 ARG 0.008 0.000 ARG B 488 TYR 0.012 0.001 TYR F 420 PHE 0.018 0.001 PHE F 692 TRP 0.020 0.002 TRP E 290 HIS 0.009 0.001 HIS B 543 Details of bonding type rmsd covalent geometry : bond 0.00655 (34146) covalent geometry : angle 0.75227 (46362) hydrogen bonds : bond 0.14356 ( 1924) hydrogen bonds : angle 5.96215 ( 5592) *********************** 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 : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 0.9129 time to fit residues: 200.6931 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 : 1.098 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.8980 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 5.9990 chunk 424 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 overall best weight: 2.8584 ------------------------------------------------------------------------------- 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** A 560 HIS F 332 ASN ** F 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 560 HIS 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** D 560 HIS C 332 ASN ** C 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 560 HIS B 332 ASN ** B 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.092927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.065942 restraints weight = 81511.881| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.87 r_work: 0.2766 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 34146 Z= 0.221 Angle : 0.607 10.076 46362 Z= 0.303 Chirality : 0.041 0.158 5166 Planarity : 0.004 0.045 6186 Dihedral : 4.160 35.195 4803 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.88 % Allowed : 6.57 % Favored : 92.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.13), residues: 4302 helix: 1.59 (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 ARG 0.008 0.000 ARG B 516 TYR 0.014 0.001 TYR A 50 PHE 0.013 0.001 PHE C 692 TRP 0.015 0.002 TRP D 205 HIS 0.011 0.001 HIS E 543 Details of bonding type rmsd covalent geometry : bond 0.00504 (34146) covalent geometry : angle 0.60692 (46362) hydrogen bonds : bond 0.04605 ( 1924) hydrogen bonds : angle 4.78580 ( 5592) *********************** 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 138 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 10 residues processed: 128 average time/residue: 0.7898 time to fit residues: 119.1506 Evaluate side-chains 99 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 1.176 ------------------------------------------------------------------------------- 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 F residue 433 MET Chi-restraints excluded: chain E 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 Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain B residue 315 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 420 optimal weight: 0.7980 chunk 249 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 338 optimal weight: 0.9980 chunk 246 optimal weight: 0.0970 chunk 23 optimal weight: 8.9990 chunk 160 optimal weight: 20.0000 chunk 95 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 308 optimal weight: 4.9990 chunk 198 optimal weight: 6.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.083655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.057923 restraints weight = 80997.825| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.79 r_work: 0.2809 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 34146 Z= 0.117 Angle : 0.527 10.250 46362 Z= 0.262 Chirality : 0.039 0.152 5166 Planarity : 0.003 0.044 6186 Dihedral : 4.000 20.188 4800 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.94 % Allowed : 8.54 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.13), residues: 4302 helix: 1.72 (0.11), residues: 2310 sheet: 0.18 (0.22), residues: 546 loop : 0.35 (0.18), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 200 TYR 0.012 0.001 TYR D 50 PHE 0.015 0.001 PHE A 692 TRP 0.017 0.001 TRP F 290 HIS 0.008 0.000 HIS B 543 Details of bonding type rmsd covalent geometry : bond 0.00251 (34146) covalent geometry : angle 0.52687 (46362) hydrogen bonds : bond 0.03985 ( 1924) hydrogen bonds : angle 4.44743 ( 5592) *********************** 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 138 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 106 time to evaluate : 1.184 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 outliers start: 32 outliers final: 15 residues processed: 132 average time/residue: 0.7285 time to fit residues: 113.5778 Evaluate side-chains 104 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 1.129 ------------------------------------------------------------------------------- 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 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 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 53 optimal weight: 0.0980 chunk 38 optimal weight: 3.9990 chunk 202 optimal weight: 7.9990 chunk 142 optimal weight: 10.0000 chunk 379 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 216 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 342 GLN ** C 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.082455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.056087 restraints weight = 81373.680| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.79 r_work: 0.2769 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 34146 Z= 0.178 Angle : 0.543 9.354 46362 Z= 0.269 Chirality : 0.039 0.162 5166 Planarity : 0.003 0.048 6186 Dihedral : 3.958 20.088 4800 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.06 % Allowed : 9.80 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.13), residues: 4302 helix: 1.79 (0.11), residues: 2346 sheet: 0.26 (0.22), residues: 546 loop : 0.43 (0.18), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 200 TYR 0.013 0.001 TYR A 50 PHE 0.016 0.001 PHE C 692 TRP 0.025 0.001 TRP C 290 HIS 0.011 0.001 HIS B 543 Details of bonding type rmsd covalent geometry : bond 0.00404 (34146) covalent geometry : angle 0.54297 (46362) hydrogen bonds : bond 0.03899 ( 1924) hydrogen bonds : angle 4.32446 ( 5592) *********************** 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 131 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 95 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 693 ARG cc_start: 0.8193 (mtm-85) cc_final: 0.7544 (ptp90) REVERT: F 141 GLN cc_start: 0.9465 (tm-30) cc_final: 0.9127 (tm-30) REVERT: D 693 ARG cc_start: 0.8174 (mtm-85) cc_final: 0.7524 (ptp90) outliers start: 36 outliers final: 20 residues processed: 123 average time/residue: 0.6357 time to fit residues: 93.5204 Evaluate side-chains 107 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 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 183 VAL Chi-restraints excluded: chain C residue 342 GLN 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 646 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 102 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 188 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 268 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3466 r_free = 0.3466 target = 0.082850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.056266 restraints weight = 80928.616| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.81 r_work: 0.2780 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 34146 Z= 0.143 Angle : 0.519 9.769 46362 Z= 0.257 Chirality : 0.038 0.156 5166 Planarity : 0.003 0.044 6186 Dihedral : 3.919 19.962 4800 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.09 % Allowed : 10.50 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.13), residues: 4302 helix: 1.85 (0.11), residues: 2340 sheet: 0.34 (0.22), residues: 546 loop : 0.44 (0.18), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 516 TYR 0.013 0.001 TYR D 50 PHE 0.016 0.001 PHE C 692 TRP 0.022 0.001 TRP F 290 HIS 0.009 0.001 HIS B 543 Details of bonding type rmsd covalent geometry : bond 0.00321 (34146) covalent geometry : angle 0.51880 (46362) hydrogen bonds : bond 0.03752 ( 1924) hydrogen bonds : angle 4.24662 ( 5592) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 96 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 693 ARG cc_start: 0.8185 (mtm-85) cc_final: 0.7526 (ptp90) REVERT: D 693 ARG cc_start: 0.8173 (mtm-85) cc_final: 0.7513 (ptp90) REVERT: C 141 GLN cc_start: 0.9484 (tm-30) cc_final: 0.9154 (tm-30) outliers start: 37 outliers final: 23 residues processed: 124 average time/residue: 0.6656 time to fit residues: 98.3504 Evaluate side-chains 110 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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 285 VAL Chi-restraints excluded: chain F residue 342 GLN 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 315 LEU Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 716 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 349 optimal weight: 0.9980 chunk 90 optimal weight: 9.9990 chunk 405 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 365 optimal weight: 8.9990 chunk 185 optimal weight: 8.9990 chunk 55 optimal weight: 0.8980 chunk 219 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 236 optimal weight: 10.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 342 GLN ** F 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 ASN C 342 GLN ** C 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.082761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.056504 restraints weight = 81049.477| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.78 r_work: 0.2770 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 34146 Z= 0.151 Angle : 0.521 9.640 46362 Z= 0.258 Chirality : 0.038 0.155 5166 Planarity : 0.003 0.065 6186 Dihedral : 3.897 19.747 4800 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.58 % Allowed : 10.68 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.13), residues: 4302 helix: 1.90 (0.11), residues: 2346 sheet: 0.39 (0.22), residues: 546 loop : 0.45 (0.18), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 516 TYR 0.013 0.001 TYR A 50 PHE 0.017 0.001 PHE C 692 TRP 0.020 0.001 TRP F 290 HIS 0.008 0.001 HIS B 543 Details of bonding type rmsd covalent geometry : bond 0.00341 (34146) covalent geometry : angle 0.52069 (46362) hydrogen bonds : bond 0.03699 ( 1924) hydrogen bonds : angle 4.19139 ( 5592) *********************** 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 148 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 94 time to evaluate : 1.306 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 outliers start: 54 outliers final: 27 residues processed: 138 average time/residue: 0.6123 time to fit residues: 102.5032 Evaluate side-chains 115 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 88 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 603 ASP Chi-restraints excluded: chain F residue 716 GLU Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 716 GLU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain 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 96 optimal weight: 10.0000 chunk 256 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 156 optimal weight: 20.0000 chunk 346 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 394 optimal weight: 2.9990 chunk 373 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 37 optimal weight: 0.1980 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN F 342 GLN ** F 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.081725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.055270 restraints weight = 81796.151| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.79 r_work: 0.2747 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 34146 Z= 0.224 Angle : 0.572 10.232 46362 Z= 0.283 Chirality : 0.040 0.161 5166 Planarity : 0.003 0.048 6186 Dihedral : 3.965 19.796 4800 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.32 % Allowed : 11.24 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.13), residues: 4302 helix: 1.90 (0.11), residues: 2352 sheet: 0.39 (0.22), residues: 546 loop : 0.46 (0.18), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 693 TYR 0.014 0.001 TYR D 50 PHE 0.018 0.001 PHE F 692 TRP 0.021 0.001 TRP C 290 HIS 0.010 0.001 HIS D 543 Details of bonding type rmsd covalent geometry : bond 0.00512 (34146) covalent geometry : angle 0.57176 (46362) hydrogen bonds : bond 0.03819 ( 1924) hydrogen bonds : angle 4.22649 ( 5592) *********************** 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 137 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 92 time to evaluate : 1.203 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: F 141 GLN cc_start: 0.9501 (tm-30) cc_final: 0.9176 (tm-30) REVERT: C 141 GLN cc_start: 0.9489 (tm-30) cc_final: 0.9155 (tm-30) REVERT: C 690 GLU cc_start: 0.8455 (mp0) cc_final: 0.8143 (pm20) outliers start: 45 outliers final: 35 residues processed: 131 average time/residue: 0.5354 time to fit residues: 85.7445 Evaluate side-chains 122 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 87 time to evaluate : 1.211 ------------------------------------------------------------------------------- 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 349 VAL 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 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 349 VAL Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 349 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 349 VAL Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 349 VAL 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 204 optimal weight: 0.9980 chunk 181 optimal weight: 0.9980 chunk 225 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 209 optimal weight: 1.9990 chunk 274 optimal weight: 0.9990 chunk 189 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 373 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 chunk 196 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 342 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.083183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.056752 restraints weight = 80638.281| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.81 r_work: 0.2787 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34146 Z= 0.121 Angle : 0.531 10.280 46362 Z= 0.262 Chirality : 0.038 0.158 5166 Planarity : 0.003 0.041 6186 Dihedral : 3.902 25.471 4800 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.12 % Allowed : 11.74 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.86 (0.13), residues: 4302 helix: 1.95 (0.11), residues: 2346 sheet: 0.43 (0.22), residues: 546 loop : 0.48 (0.18), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 688 TYR 0.012 0.001 TYR F 50 PHE 0.018 0.001 PHE C 692 TRP 0.018 0.001 TRP C 290 HIS 0.007 0.001 HIS D 543 Details of bonding type rmsd covalent geometry : bond 0.00269 (34146) covalent geometry : angle 0.53140 (46362) hydrogen bonds : bond 0.03601 ( 1924) hydrogen bonds : angle 4.11578 ( 5592) *********************** 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 140 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 102 time to evaluate : 0.947 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 342 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8716 (pm20) REVERT: E 356 MET cc_start: 0.9447 (pmt) cc_final: 0.8083 (pmt) REVERT: C 342 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8730 (pm20) outliers start: 38 outliers final: 22 residues processed: 140 average time/residue: 0.5638 time to fit residues: 95.3287 Evaluate side-chains 110 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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 285 VAL Chi-restraints excluded: chain F residue 342 GLN 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 603 ASP Chi-restraints excluded: chain D residue 716 GLU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 342 GLN Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 716 GLU Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 646 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 307 optimal weight: 10.0000 chunk 151 optimal weight: 6.9990 chunk 394 optimal weight: 0.8980 chunk 383 optimal weight: 2.9990 chunk 277 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 247 optimal weight: 10.0000 chunk 159 optimal weight: 7.9990 chunk 319 optimal weight: 1.9990 chunk 323 optimal weight: 0.2980 chunk 225 optimal weight: 8.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 GLN ** F 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3465 r_free = 0.3465 target = 0.082566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.056150 restraints weight = 80710.794| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.81 r_work: 0.2773 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 34146 Z= 0.157 Angle : 0.548 10.471 46362 Z= 0.271 Chirality : 0.038 0.153 5166 Planarity : 0.003 0.044 6186 Dihedral : 3.899 24.993 4800 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.06 % Allowed : 12.09 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.13), residues: 4302 helix: 1.98 (0.11), residues: 2346 sheet: 0.43 (0.22), residues: 546 loop : 0.51 (0.18), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 200 TYR 0.012 0.001 TYR D 50 PHE 0.019 0.001 PHE F 692 TRP 0.026 0.001 TRP C 290 HIS 0.008 0.001 HIS D 543 Details of bonding type rmsd covalent geometry : bond 0.00358 (34146) covalent geometry : angle 0.54763 (46362) hydrogen bonds : bond 0.03623 ( 1924) hydrogen bonds : angle 4.10330 ( 5592) *********************** 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 128 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 92 time to evaluate : 0.937 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: F 141 GLN cc_start: 0.9511 (tm-30) cc_final: 0.9192 (tm-30) REVERT: E 356 MET cc_start: 0.9453 (pmt) cc_final: 0.8070 (pmt) REVERT: C 141 GLN cc_start: 0.9507 (tm-30) cc_final: 0.9186 (tm-30) REVERT: B 200 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8562 (tpt90) outliers start: 36 outliers final: 24 residues processed: 124 average time/residue: 0.5579 time to fit residues: 83.1860 Evaluate side-chains 111 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 603 ASP Chi-restraints excluded: chain 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 603 ASP Chi-restraints excluded: chain D residue 716 GLU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 716 GLU Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 200 ARG Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 646 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 177 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 363 optimal weight: 0.0670 chunk 263 optimal weight: 5.9990 chunk 214 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 425 optimal weight: 2.9990 chunk 247 optimal weight: 10.0000 chunk 244 optimal weight: 0.5980 overall best weight: 1.9324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 160 ASN F 540 GLN ** F 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN 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 = 0.3465 r_free = 0.3465 target = 0.082422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.055876 restraints weight = 81032.051| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.81 r_work: 0.2765 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 34146 Z= 0.162 Angle : 0.555 10.558 46362 Z= 0.275 Chirality : 0.039 0.153 5166 Planarity : 0.003 0.041 6186 Dihedral : 3.908 25.560 4800 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.94 % Allowed : 12.38 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.13), residues: 4302 helix: 1.99 (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 ARG 0.010 0.000 ARG F 200 TYR 0.012 0.001 TYR D 50 PHE 0.017 0.001 PHE F 692 TRP 0.016 0.001 TRP C 290 HIS 0.009 0.001 HIS D 543 Details of bonding type rmsd covalent geometry : bond 0.00369 (34146) covalent geometry : angle 0.55456 (46362) hydrogen bonds : bond 0.03627 ( 1924) hydrogen bonds : angle 4.09875 ( 5592) ********************** 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 121 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 89 time to evaluate : 1.203 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: 0.9512 (tm-30) cc_final: 0.9195 (tm-30) REVERT: E 356 MET cc_start: 0.9458 (pmt) cc_final: 0.8071 (pmt) REVERT: C 141 GLN cc_start: 0.9508 (tm-30) cc_final: 0.9188 (tm-30) REVERT: B 200 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8556 (tpt90) outliers start: 32 outliers final: 24 residues processed: 114 average time/residue: 0.5960 time to fit residues: 82.3354 Evaluate side-chains 111 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 603 ASP Chi-restraints excluded: chain 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 603 ASP Chi-restraints excluded: chain D residue 716 GLU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 716 GLU Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 200 ARG Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 646 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 12 optimal weight: 8.9990 chunk 86 optimal weight: 8.9990 chunk 60 optimal weight: 7.9990 chunk 330 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 394 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 264 optimal weight: 5.9990 chunk 417 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.3418 r_free = 0.3418 target = 0.080267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.053223 restraints weight = 81338.149| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.80 r_work: 0.2703 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 34146 Z= 0.337 Angle : 0.658 9.835 46362 Z= 0.327 Chirality : 0.042 0.154 5166 Planarity : 0.004 0.047 6186 Dihedral : 4.098 24.966 4800 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.06 % Allowed : 12.32 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.13), residues: 4302 helix: 1.88 (0.11), residues: 2352 sheet: 0.46 (0.22), residues: 534 loop : 0.43 (0.18), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 200 TYR 0.016 0.002 TYR E 557 PHE 0.022 0.002 PHE F 692 TRP 0.023 0.002 TRP C 290 HIS 0.016 0.001 HIS A 543 Details of bonding type rmsd covalent geometry : bond 0.00775 (34146) covalent geometry : angle 0.65758 (46362) hydrogen bonds : bond 0.04050 ( 1924) hydrogen bonds : angle 4.30937 ( 5592) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6988.50 seconds wall clock time: 120 minutes 28.26 seconds (7228.26 seconds total)