Starting phenix.real_space_refine on Sat Jun 21 13:20:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j5z_35996/06_2025/8j5z_35996.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j5z_35996/06_2025/8j5z_35996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j5z_35996/06_2025/8j5z_35996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j5z_35996/06_2025/8j5z_35996.map" model { file = "/net/cci-nas-00/data/ceres_data/8j5z_35996/06_2025/8j5z_35996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j5z_35996/06_2025/8j5z_35996.cif" } resolution = 4.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 4 Type Number sf(0) Gaussians S 164 5.16 5 C 16000 2.51 5 N 4184 2.21 5 O 4508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24856 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 6194 Classifications: {'peptide': 764} Link IDs: {'PTRANS': 43, 'TRANS': 720} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 6194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 6194 Classifications: {'peptide': 764} Link IDs: {'PTRANS': 43, 'TRANS': 720} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 6194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 6194 Classifications: {'peptide': 764} Link IDs: {'PTRANS': 43, 'TRANS': 720} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 6194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 6194 Classifications: {'peptide': 764} Link IDs: {'PTRANS': 43, 'TRANS': 720} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'BOG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'BOG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'BOG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'BOG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.25, per 1000 atoms: 0.53 Number of scatterers: 24856 At special positions: 0 Unit cell: (176.55, 170.13, 117.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 164 16.00 O 4508 8.00 N 4184 7.00 C 16000 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: 5.81 Conformation dependent library (CDL) restraints added in 3.3 seconds 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5656 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 12 sheets defined 54.3% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.49 Creating SS restraints... Processing helix chain 'A' and resid 42 through 56 removed outlier: 4.225A pdb=" N GLU A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A 47 " --> pdb=" O ALA A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 75 removed outlier: 4.024A pdb=" N MET A 68 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE A 71 " --> pdb=" O TRP A 67 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N MET A 72 " --> pdb=" O MET A 68 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG A 73 " --> pdb=" O MET A 69 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLU A 74 " --> pdb=" O GLN A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 112 removed outlier: 3.724A pdb=" N LEU A 97 " --> pdb=" O THR A 93 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN A 106 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHE A 107 " --> pdb=" O ARG A 103 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE A 108 " --> pdb=" O THR A 104 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLN A 112 " --> pdb=" O PHE A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 139 removed outlier: 3.778A pdb=" N PHE A 132 " --> pdb=" O PHE A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 146 Processing helix chain 'A' and resid 147 through 161 removed outlier: 3.677A pdb=" N LYS A 152 " --> pdb=" O PRO A 148 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N HIS A 161 " --> pdb=" O PHE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 191 removed outlier: 3.637A pdb=" N LEU A 191 " --> pdb=" O CYS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 212 removed outlier: 3.655A pdb=" N LYS A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TRP A 209 " --> pdb=" O ARG A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 230 removed outlier: 3.532A pdb=" N ILE A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.602A pdb=" N CYS A 238 " --> pdb=" O TRP A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 247 removed outlier: 4.251A pdb=" N PHE A 245 " --> pdb=" O PRO A 242 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N TRP A 246 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 277 Proline residue: A 269 - end of helix Processing helix chain 'A' and resid 283 through 294 removed outlier: 4.301A pdb=" N GLU A 291 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLU A 292 " --> pdb=" O GLN A 288 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N HIS A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 335 removed outlier: 3.549A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 365 removed outlier: 3.547A pdb=" N ASN A 364 " --> pdb=" O TYR A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 386 removed outlier: 3.694A pdb=" N GLU A 385 " --> pdb=" O CYS A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 398 Processing helix chain 'A' and resid 399 through 401 No H-bonds generated for 'chain 'A' and resid 399 through 401' Processing helix chain 'A' and resid 417 through 432 Processing helix chain 'A' and resid 439 through 453 removed outlier: 4.095A pdb=" N PHE A 449 " --> pdb=" O LYS A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 502 removed outlier: 3.650A pdb=" N GLU A 492 " --> pdb=" O ASP A 488 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR A 502 " --> pdb=" O LEU A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 509 Processing helix chain 'A' and resid 515 through 527 removed outlier: 4.215A pdb=" N GLU A 519 " --> pdb=" O GLU A 515 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A 520 " --> pdb=" O TRP A 516 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 550 removed outlier: 3.854A pdb=" N MET A 546 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU A 547 " --> pdb=" O GLU A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 582 removed outlier: 3.873A pdb=" N LYS A 580 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A 581 " --> pdb=" O SER A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 604 removed outlier: 3.899A pdb=" N ASP A 591 " --> pdb=" O THR A 587 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASN A 592 " --> pdb=" O LYS A 588 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG A 599 " --> pdb=" O ARG A 595 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR A 600 " --> pdb=" O ASN A 596 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 601 " --> pdb=" O ALA A 597 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU A 602 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP A 603 " --> pdb=" O ARG A 599 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 604 " --> pdb=" O TYR A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 631 removed outlier: 3.853A pdb=" N PHE A 625 " --> pdb=" O TYR A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 634 No H-bonds generated for 'chain 'A' and resid 632 through 634' Processing helix chain 'A' and resid 642 through 653 removed outlier: 4.191A pdb=" N GLY A 646 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL A 647 " --> pdb=" O VAL A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 681 through 694 Processing helix chain 'A' and resid 702 through 714 removed outlier: 4.137A pdb=" N ARG A 707 " --> pdb=" O THR A 703 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU A 712 " --> pdb=" O GLY A 708 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE A 713 " --> pdb=" O ALA A 709 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN A 714 " --> pdb=" O LYS A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 758 removed outlier: 3.901A pdb=" N PHE A 746 " --> pdb=" O TYR A 742 " (cutoff:3.500A) Proline residue: A 747 - end of helix removed outlier: 3.718A pdb=" N ARG A 755 " --> pdb=" O LEU A 751 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS A 756 " --> pdb=" O GLY A 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 56 removed outlier: 4.225A pdb=" N GLU B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU B 47 " --> pdb=" O ALA B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 75 removed outlier: 4.023A pdb=" N MET B 68 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE B 71 " --> pdb=" O TRP B 67 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N MET B 72 " --> pdb=" O MET B 68 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ARG B 73 " --> pdb=" O MET B 69 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLU B 74 " --> pdb=" O GLN B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 112 removed outlier: 3.723A pdb=" N LEU B 97 " --> pdb=" O THR B 93 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN B 106 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE B 107 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE B 108 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLN B 112 " --> pdb=" O PHE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 139 removed outlier: 3.778A pdb=" N PHE B 132 " --> pdb=" O PHE B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 146 Processing helix chain 'B' and resid 147 through 161 removed outlier: 3.678A pdb=" N LYS B 152 " --> pdb=" O PRO B 148 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU B 153 " --> pdb=" O GLU B 149 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N HIS B 161 " --> pdb=" O PHE B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 191 removed outlier: 3.636A pdb=" N LEU B 191 " --> pdb=" O CYS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 212 removed outlier: 3.655A pdb=" N LYS B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TRP B 209 " --> pdb=" O ARG B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 230 removed outlier: 3.532A pdb=" N ILE B 229 " --> pdb=" O THR B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 238 removed outlier: 3.603A pdb=" N CYS B 238 " --> pdb=" O TRP B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 247 removed outlier: 4.251A pdb=" N PHE B 245 " --> pdb=" O PRO B 242 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N TRP B 246 " --> pdb=" O PRO B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 277 Proline residue: B 269 - end of helix Processing helix chain 'B' and resid 283 through 294 removed outlier: 4.301A pdb=" N GLU B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N GLU B 292 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU B 293 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N HIS B 294 " --> pdb=" O ARG B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 335 removed outlier: 3.549A pdb=" N VAL B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 365 removed outlier: 3.546A pdb=" N ASN B 364 " --> pdb=" O TYR B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 386 removed outlier: 3.694A pdb=" N GLU B 385 " --> pdb=" O CYS B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 398 Processing helix chain 'B' and resid 399 through 401 No H-bonds generated for 'chain 'B' and resid 399 through 401' Processing helix chain 'B' and resid 417 through 432 Processing helix chain 'B' and resid 439 through 453 removed outlier: 4.095A pdb=" N PHE B 449 " --> pdb=" O LYS B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 502 removed outlier: 3.650A pdb=" N GLU B 492 " --> pdb=" O ASP B 488 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR B 502 " --> pdb=" O LEU B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 509 Processing helix chain 'B' and resid 515 through 527 removed outlier: 4.214A pdb=" N GLU B 519 " --> pdb=" O GLU B 515 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B 520 " --> pdb=" O TRP B 516 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 527 " --> pdb=" O ILE B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 550 removed outlier: 3.853A pdb=" N MET B 546 " --> pdb=" O GLY B 543 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU B 547 " --> pdb=" O GLU B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 582 removed outlier: 3.874A pdb=" N LYS B 580 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU B 581 " --> pdb=" O SER B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 604 removed outlier: 3.900A pdb=" N ASP B 591 " --> pdb=" O THR B 587 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASN B 592 " --> pdb=" O LYS B 588 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG B 599 " --> pdb=" O ARG B 595 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR B 600 " --> pdb=" O ASN B 596 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU B 601 " --> pdb=" O ALA B 597 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU B 602 " --> pdb=" O ILE B 598 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP B 603 " --> pdb=" O ARG B 599 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 604 " --> pdb=" O TYR B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 631 removed outlier: 3.853A pdb=" N PHE B 625 " --> pdb=" O TYR B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 634 No H-bonds generated for 'chain 'B' and resid 632 through 634' Processing helix chain 'B' and resid 642 through 653 removed outlier: 4.191A pdb=" N GLY B 646 " --> pdb=" O ALA B 642 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL B 647 " --> pdb=" O VAL B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 670 Processing helix chain 'B' and resid 681 through 694 Processing helix chain 'B' and resid 702 through 714 removed outlier: 4.138A pdb=" N ARG B 707 " --> pdb=" O THR B 703 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU B 712 " --> pdb=" O GLY B 708 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE B 713 " --> pdb=" O ALA B 709 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN B 714 " --> pdb=" O LYS B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 758 removed outlier: 3.902A pdb=" N PHE B 746 " --> pdb=" O TYR B 742 " (cutoff:3.500A) Proline residue: B 747 - end of helix removed outlier: 3.717A pdb=" N ARG B 755 " --> pdb=" O LEU B 751 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS B 756 " --> pdb=" O GLY B 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 56 removed outlier: 4.224A pdb=" N GLU C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU C 47 " --> pdb=" O ALA C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 75 removed outlier: 4.023A pdb=" N MET C 68 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE C 71 " --> pdb=" O TRP C 67 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET C 72 " --> pdb=" O MET C 68 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ARG C 73 " --> pdb=" O MET C 69 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLU C 74 " --> pdb=" O GLN C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 112 removed outlier: 3.723A pdb=" N LEU C 97 " --> pdb=" O THR C 93 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN C 106 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE C 107 " --> pdb=" O ARG C 103 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE C 108 " --> pdb=" O THR C 104 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLN C 112 " --> pdb=" O PHE C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 139 removed outlier: 3.777A pdb=" N PHE C 132 " --> pdb=" O PHE C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 146 Processing helix chain 'C' and resid 147 through 161 removed outlier: 3.676A pdb=" N LYS C 152 " --> pdb=" O PRO C 148 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU C 153 " --> pdb=" O GLU C 149 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N HIS C 161 " --> pdb=" O PHE C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 191 removed outlier: 3.636A pdb=" N LEU C 191 " --> pdb=" O CYS C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 212 removed outlier: 3.656A pdb=" N LYS C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TRP C 209 " --> pdb=" O ARG C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 230 removed outlier: 3.533A pdb=" N ILE C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 238 removed outlier: 3.603A pdb=" N CYS C 238 " --> pdb=" O TRP C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 247 removed outlier: 4.251A pdb=" N PHE C 245 " --> pdb=" O PRO C 242 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N TRP C 246 " --> pdb=" O PRO C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 277 Proline residue: C 269 - end of helix Processing helix chain 'C' and resid 283 through 294 removed outlier: 4.301A pdb=" N GLU C 291 " --> pdb=" O LEU C 287 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLU C 292 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU C 293 " --> pdb=" O LEU C 289 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N HIS C 294 " --> pdb=" O ARG C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 335 removed outlier: 3.548A pdb=" N VAL C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 365 removed outlier: 3.547A pdb=" N ASN C 364 " --> pdb=" O TYR C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 386 removed outlier: 3.694A pdb=" N GLU C 385 " --> pdb=" O CYS C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 398 Processing helix chain 'C' and resid 399 through 401 No H-bonds generated for 'chain 'C' and resid 399 through 401' Processing helix chain 'C' and resid 417 through 432 Processing helix chain 'C' and resid 439 through 453 removed outlier: 4.096A pdb=" N PHE C 449 " --> pdb=" O LYS C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 502 removed outlier: 3.651A pdb=" N GLU C 492 " --> pdb=" O ASP C 488 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR C 502 " --> pdb=" O LEU C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 509 Processing helix chain 'C' and resid 515 through 527 removed outlier: 4.214A pdb=" N GLU C 519 " --> pdb=" O GLU C 515 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA C 520 " --> pdb=" O TRP C 516 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU C 527 " --> pdb=" O ILE C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 550 removed outlier: 3.854A pdb=" N MET C 546 " --> pdb=" O GLY C 543 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU C 547 " --> pdb=" O GLU C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 582 removed outlier: 3.874A pdb=" N LYS C 580 " --> pdb=" O VAL C 576 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU C 581 " --> pdb=" O SER C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 604 removed outlier: 3.900A pdb=" N ASP C 591 " --> pdb=" O THR C 587 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ASN C 592 " --> pdb=" O LYS C 588 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG C 599 " --> pdb=" O ARG C 595 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR C 600 " --> pdb=" O ASN C 596 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU C 601 " --> pdb=" O ALA C 597 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU C 602 " --> pdb=" O ILE C 598 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP C 603 " --> pdb=" O ARG C 599 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C 604 " --> pdb=" O TYR C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 631 removed outlier: 3.853A pdb=" N PHE C 625 " --> pdb=" O TYR C 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 634 No H-bonds generated for 'chain 'C' and resid 632 through 634' Processing helix chain 'C' and resid 642 through 653 removed outlier: 4.191A pdb=" N GLY C 646 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL C 647 " --> pdb=" O VAL C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 670 Processing helix chain 'C' and resid 681 through 694 Processing helix chain 'C' and resid 702 through 714 removed outlier: 4.137A pdb=" N ARG C 707 " --> pdb=" O THR C 703 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU C 712 " --> pdb=" O GLY C 708 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE C 713 " --> pdb=" O ALA C 709 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN C 714 " --> pdb=" O LYS C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 758 removed outlier: 3.902A pdb=" N PHE C 746 " --> pdb=" O TYR C 742 " (cutoff:3.500A) Proline residue: C 747 - end of helix removed outlier: 3.718A pdb=" N ARG C 755 " --> pdb=" O LEU C 751 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS C 756 " --> pdb=" O GLY C 752 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 56 removed outlier: 4.225A pdb=" N GLU D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU D 47 " --> pdb=" O ALA D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 75 removed outlier: 4.023A pdb=" N MET D 68 " --> pdb=" O ASP D 64 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE D 71 " --> pdb=" O TRP D 67 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET D 72 " --> pdb=" O MET D 68 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ARG D 73 " --> pdb=" O MET D 69 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLU D 74 " --> pdb=" O GLN D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 112 removed outlier: 3.723A pdb=" N LEU D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN D 106 " --> pdb=" O THR D 102 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE D 107 " --> pdb=" O ARG D 103 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE D 108 " --> pdb=" O THR D 104 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLN D 112 " --> pdb=" O PHE D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 139 removed outlier: 3.778A pdb=" N PHE D 132 " --> pdb=" O PHE D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 146 Processing helix chain 'D' and resid 147 through 161 removed outlier: 3.677A pdb=" N LYS D 152 " --> pdb=" O PRO D 148 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU D 153 " --> pdb=" O GLU D 149 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N HIS D 161 " --> pdb=" O PHE D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 191 removed outlier: 3.636A pdb=" N LEU D 191 " --> pdb=" O CYS D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 212 removed outlier: 3.655A pdb=" N LYS D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TRP D 209 " --> pdb=" O ARG D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 230 removed outlier: 3.533A pdb=" N ILE D 229 " --> pdb=" O THR D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 238 removed outlier: 3.602A pdb=" N CYS D 238 " --> pdb=" O TRP D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 247 removed outlier: 4.251A pdb=" N PHE D 245 " --> pdb=" O PRO D 242 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N TRP D 246 " --> pdb=" O PRO D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 277 Proline residue: D 269 - end of helix Processing helix chain 'D' and resid 283 through 294 removed outlier: 4.301A pdb=" N GLU D 291 " --> pdb=" O LEU D 287 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLU D 292 " --> pdb=" O GLN D 288 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU D 293 " --> pdb=" O LEU D 289 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N HIS D 294 " --> pdb=" O ARG D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 335 removed outlier: 3.548A pdb=" N VAL D 332 " --> pdb=" O ASP D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 365 removed outlier: 3.547A pdb=" N ASN D 364 " --> pdb=" O TYR D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 386 removed outlier: 3.694A pdb=" N GLU D 385 " --> pdb=" O CYS D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 398 Processing helix chain 'D' and resid 399 through 401 No H-bonds generated for 'chain 'D' and resid 399 through 401' Processing helix chain 'D' and resid 417 through 432 Processing helix chain 'D' and resid 439 through 453 removed outlier: 4.095A pdb=" N PHE D 449 " --> pdb=" O LYS D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 502 removed outlier: 3.650A pdb=" N GLU D 492 " --> pdb=" O ASP D 488 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR D 502 " --> pdb=" O LEU D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 509 Processing helix chain 'D' and resid 515 through 527 removed outlier: 4.214A pdb=" N GLU D 519 " --> pdb=" O GLU D 515 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA D 520 " --> pdb=" O TRP D 516 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU D 527 " --> pdb=" O ILE D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 550 removed outlier: 3.854A pdb=" N MET D 546 " --> pdb=" O GLY D 543 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU D 547 " --> pdb=" O GLU D 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 582 removed outlier: 3.874A pdb=" N LYS D 580 " --> pdb=" O VAL D 576 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU D 581 " --> pdb=" O SER D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 604 removed outlier: 3.899A pdb=" N ASP D 591 " --> pdb=" O THR D 587 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASN D 592 " --> pdb=" O LYS D 588 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG D 599 " --> pdb=" O ARG D 595 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR D 600 " --> pdb=" O ASN D 596 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU D 601 " --> pdb=" O ALA D 597 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU D 602 " --> pdb=" O ILE D 598 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP D 603 " --> pdb=" O ARG D 599 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL D 604 " --> pdb=" O TYR D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 631 removed outlier: 3.853A pdb=" N PHE D 625 " --> pdb=" O TYR D 621 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 634 No H-bonds generated for 'chain 'D' and resid 632 through 634' Processing helix chain 'D' and resid 642 through 653 removed outlier: 4.191A pdb=" N GLY D 646 " --> pdb=" O ALA D 642 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL D 647 " --> pdb=" O VAL D 643 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 670 Processing helix chain 'D' and resid 681 through 694 Processing helix chain 'D' and resid 702 through 714 removed outlier: 4.137A pdb=" N ARG D 707 " --> pdb=" O THR D 703 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU D 712 " --> pdb=" O GLY D 708 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE D 713 " --> pdb=" O ALA D 709 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN D 714 " --> pdb=" O LYS D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 758 removed outlier: 3.902A pdb=" N PHE D 746 " --> pdb=" O TYR D 742 " (cutoff:3.500A) Proline residue: D 747 - end of helix removed outlier: 3.718A pdb=" N ARG D 755 " --> pdb=" O LEU D 751 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS D 756 " --> pdb=" O GLY D 752 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 6 removed outlier: 3.771A pdb=" N GLU A 31 " --> pdb=" O LYS A 3 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS A 5 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N THR A 29 " --> pdb=" O LYS A 5 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA3, first strand: chain 'A' and resid 730 through 731 Processing sheet with id=AA4, first strand: chain 'B' and resid 2 through 6 removed outlier: 3.772A pdb=" N GLU B 31 " --> pdb=" O LYS B 3 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS B 5 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR B 29 " --> pdb=" O LYS B 5 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 403 through 404 Processing sheet with id=AA6, first strand: chain 'B' and resid 730 through 731 Processing sheet with id=AA7, first strand: chain 'C' and resid 2 through 6 removed outlier: 3.771A pdb=" N GLU C 31 " --> pdb=" O LYS C 3 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS C 5 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR C 29 " --> pdb=" O LYS C 5 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 403 through 404 Processing sheet with id=AA9, first strand: chain 'C' and resid 730 through 731 Processing sheet with id=AB1, first strand: chain 'D' and resid 2 through 6 removed outlier: 3.771A pdb=" N GLU D 31 " --> pdb=" O LYS D 3 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS D 5 " --> pdb=" O THR D 29 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N THR D 29 " --> pdb=" O LYS D 5 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 403 through 404 Processing sheet with id=AB3, first strand: chain 'D' and resid 730 through 731 916 hydrogen bonds defined for protein. 2664 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: 7.27 Time building geometry restraints manager: 6.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7918 1.34 - 1.46: 6406 1.46 - 1.58: 11040 1.58 - 1.69: 0 1.69 - 1.81: 256 Bond restraints: 25620 Sorted by residual: bond pdb=" C1 BOG C 801 " pdb=" O1 BOG C 801 " ideal model delta sigma weight residual 1.372 1.431 -0.059 2.00e-02 2.50e+03 8.61e+00 bond pdb=" C1 BOG D 801 " pdb=" O1 BOG D 801 " ideal model delta sigma weight residual 1.372 1.425 -0.053 2.00e-02 2.50e+03 7.09e+00 bond pdb=" C1 BOG B 801 " pdb=" O1 BOG B 801 " ideal model delta sigma weight residual 1.372 1.423 -0.051 2.00e-02 2.50e+03 6.38e+00 bond pdb=" C2 BOG D 801 " pdb=" O2 BOG D 801 " ideal model delta sigma weight residual 1.403 1.431 -0.028 2.00e-02 2.50e+03 2.02e+00 bond pdb=" C2 BOG C 801 " pdb=" O2 BOG C 801 " ideal model delta sigma weight residual 1.403 1.430 -0.027 2.00e-02 2.50e+03 1.88e+00 ... (remaining 25615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 33563 1.03 - 2.06: 905 2.06 - 3.09: 214 3.09 - 4.11: 65 4.11 - 5.14: 45 Bond angle restraints: 34792 Sorted by residual: angle pdb=" N VAL A 711 " pdb=" CA VAL A 711 " pdb=" C VAL A 711 " ideal model delta sigma weight residual 112.98 110.26 2.72 1.25e+00 6.40e-01 4.72e+00 angle pdb=" N VAL B 711 " pdb=" CA VAL B 711 " pdb=" C VAL B 711 " ideal model delta sigma weight residual 112.98 110.28 2.70 1.25e+00 6.40e-01 4.67e+00 angle pdb=" N VAL C 711 " pdb=" CA VAL C 711 " pdb=" C VAL C 711 " ideal model delta sigma weight residual 112.98 110.30 2.68 1.25e+00 6.40e-01 4.61e+00 angle pdb=" N VAL D 711 " pdb=" CA VAL D 711 " pdb=" C VAL D 711 " ideal model delta sigma weight residual 112.98 110.32 2.66 1.25e+00 6.40e-01 4.54e+00 angle pdb=" CA PRO C 130 " pdb=" C PRO C 130 " pdb=" N PRO C 131 " ideal model delta sigma weight residual 117.93 120.21 -2.28 1.20e+00 6.94e-01 3.60e+00 ... (remaining 34787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.86: 14612 24.86 - 49.72: 343 49.72 - 74.58: 71 74.58 - 99.44: 28 99.44 - 124.30: 14 Dihedral angle restraints: 15068 sinusoidal: 6200 harmonic: 8868 Sorted by residual: dihedral pdb=" C2 BOG C 801 " pdb=" C1 BOG C 801 " pdb=" O5 BOG C 801 " pdb=" C5 BOG C 801 " ideal model delta sinusoidal sigma weight residual -63.97 60.33 -124.30 1 3.00e+01 1.11e-03 1.67e+01 dihedral pdb=" C1 BOG B 801 " pdb=" C2 BOG B 801 " pdb=" C3 BOG B 801 " pdb=" O3 BOG B 801 " ideal model delta sinusoidal sigma weight residual -178.34 -56.75 -121.59 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" O2 BOG B 801 " pdb=" C2 BOG B 801 " pdb=" C3 BOG B 801 " pdb=" O3 BOG B 801 " ideal model delta sinusoidal sigma weight residual 62.09 -176.53 -121.38 1 3.00e+01 1.11e-03 1.62e+01 ... (remaining 15065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2028 0.027 - 0.054: 1010 0.054 - 0.081: 338 0.081 - 0.108: 191 0.108 - 0.135: 13 Chirality restraints: 3580 Sorted by residual: chirality pdb=" CB ILE C 368 " pdb=" CA ILE C 368 " pdb=" CG1 ILE C 368 " pdb=" CG2 ILE C 368 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CB ILE D 368 " pdb=" CA ILE D 368 " pdb=" CG1 ILE D 368 " pdb=" CG2 ILE D 368 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CB ILE B 368 " pdb=" CA ILE B 368 " pdb=" CG1 ILE B 368 " pdb=" CG2 ILE B 368 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 3577 not shown) Planarity restraints: 4452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 129 " 0.033 5.00e-02 4.00e+02 5.00e-02 4.00e+00 pdb=" N PRO A 130 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 130 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 130 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 129 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.98e+00 pdb=" N PRO D 130 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO D 130 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 130 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 129 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO B 130 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 130 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 130 " 0.028 5.00e-02 4.00e+02 ... (remaining 4449 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3863 2.76 - 3.29: 24314 3.29 - 3.83: 40638 3.83 - 4.36: 46076 4.36 - 4.90: 78965 Nonbonded interactions: 193856 Sorted by model distance: nonbonded pdb=" OG1 THR B 177 " pdb=" OD2 ASP B 314 " model vdw 2.224 3.040 nonbonded pdb=" OG1 THR A 177 " pdb=" OD2 ASP A 314 " model vdw 2.224 3.040 nonbonded pdb=" OG1 THR D 177 " pdb=" OD2 ASP D 314 " model vdw 2.224 3.040 nonbonded pdb=" OG1 THR C 177 " pdb=" OD2 ASP C 314 " model vdw 2.224 3.040 nonbonded pdb=" NH1 ARG B 645 " pdb=" OE1 GLN C 641 " model vdw 2.233 3.120 ... (remaining 193851 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: 0.17 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.030 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 51.420 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 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 : 0.002 0.059 25620 Z= 0.102 Angle : 0.468 5.142 34792 Z= 0.244 Chirality : 0.038 0.135 3580 Planarity : 0.004 0.050 4452 Dihedral : 12.557 124.298 9412 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.96 % Allowed : 8.88 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.16), residues: 3048 helix: 0.92 (0.15), residues: 1424 sheet: None (None), residues: 0 loop : -1.94 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 475 HIS 0.002 0.000 HIS C 482 PHE 0.006 0.001 PHE A 183 TYR 0.005 0.001 TYR D 582 ARG 0.001 0.000 ARG D 290 Details of bonding type rmsd hydrogen bonds : bond 0.19577 ( 916) hydrogen bonds : angle 5.03690 ( 2664) covalent geometry : bond 0.00192 (25620) covalent geometry : angle 0.46835 (34792) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.6133 (OUTLIER) cc_final: 0.5861 (pp) REVERT: A 27 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7333 (tpt90) REVERT: A 159 TYR cc_start: 0.6414 (t80) cc_final: 0.5666 (t80) REVERT: A 193 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8390 (tp) REVERT: A 270 MET cc_start: 0.7978 (mtp) cc_final: 0.7717 (mtp) REVERT: A 349 LYS cc_start: 0.7460 (mmtp) cc_final: 0.7101 (ttmt) REVERT: A 360 TYR cc_start: 0.8360 (OUTLIER) cc_final: 0.7163 (p90) REVERT: A 413 GLN cc_start: 0.7463 (tt0) cc_final: 0.7058 (tt0) REVERT: A 466 MET cc_start: 0.7962 (mmt) cc_final: 0.7599 (tpt) REVERT: A 485 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7471 (mt0) REVERT: A 486 LEU cc_start: 0.8513 (tp) cc_final: 0.8305 (tt) outliers start: 26 outliers final: 7 residues processed: 123 average time/residue: 0.2431 time to fit residues: 37.3238 Evaluate side-chains 61 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 0.0570 chunk 230 optimal weight: 20.0000 chunk 127 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 155 optimal weight: 10.0000 chunk 123 optimal weight: 0.0370 chunk 238 optimal weight: 9.9990 chunk 92 optimal weight: 0.4980 chunk 144 optimal weight: 8.9990 chunk 177 optimal weight: 8.9990 chunk 276 optimal weight: 20.0000 overall best weight: 1.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 323 GLN A 469 HIS A 480 GLN A 485 GLN A 557 ASN ** A 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.049915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.043532 restraints weight = 42571.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.044879 restraints weight = 26333.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.045770 restraints weight = 17826.103| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25620 Z= 0.121 Angle : 0.586 7.111 34792 Z= 0.301 Chirality : 0.043 0.220 3580 Planarity : 0.005 0.050 4452 Dihedral : 8.956 79.197 3492 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.15), residues: 3048 helix: 0.68 (0.14), residues: 1492 sheet: None (None), residues: 0 loop : -2.10 (0.15), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 30 HIS 0.008 0.001 HIS D 299 PHE 0.022 0.002 PHE A 183 TYR 0.021 0.001 TYR D 360 ARG 0.006 0.001 ARG D 366 Details of bonding type rmsd hydrogen bonds : bond 0.04390 ( 916) hydrogen bonds : angle 4.31632 ( 2664) covalent geometry : bond 0.00267 (25620) covalent geometry : angle 0.58594 (34792) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: A 159 TYR cc_start: 0.6682 (t80) cc_final: 0.6329 (t80) REVERT: A 230 LEU cc_start: 0.9073 (mm) cc_final: 0.8849 (mt) REVERT: A 270 MET cc_start: 0.8115 (mtp) cc_final: 0.7850 (mtp) REVERT: A 413 GLN cc_start: 0.7354 (tt0) cc_final: 0.7139 (tt0) REVERT: A 466 MET cc_start: 0.7679 (mmt) cc_final: 0.7347 (tpt) REVERT: A 499 LEU cc_start: 0.7979 (pp) cc_final: 0.7660 (pp) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1997 time to fit residues: 17.7895 Evaluate side-chains 44 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 137 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 228 optimal weight: 20.0000 chunk 117 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 75 optimal weight: 0.0030 chunk 176 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 159 optimal weight: 0.3980 overall best weight: 3.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN A 485 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.047715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.041666 restraints weight = 45601.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.042881 restraints weight = 27961.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.043743 restraints weight = 19012.212| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25620 Z= 0.121 Angle : 0.561 8.020 34792 Z= 0.282 Chirality : 0.041 0.180 3580 Planarity : 0.004 0.046 4452 Dihedral : 6.331 57.919 3492 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.15), residues: 3048 helix: 0.73 (0.14), residues: 1524 sheet: None (None), residues: 0 loop : -2.13 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 30 HIS 0.007 0.001 HIS D 299 PHE 0.014 0.001 PHE A 183 TYR 0.015 0.001 TYR B 360 ARG 0.004 0.000 ARG D 27 Details of bonding type rmsd hydrogen bonds : bond 0.03599 ( 916) hydrogen bonds : angle 4.17755 ( 2664) covalent geometry : bond 0.00276 (25620) covalent geometry : angle 0.56088 (34792) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.672 Fit side-chains REVERT: A 159 TYR cc_start: 0.6598 (t80) cc_final: 0.5961 (t80) REVERT: A 230 LEU cc_start: 0.9046 (mm) cc_final: 0.8841 (tp) REVERT: A 694 TYR cc_start: 0.8822 (m-80) cc_final: 0.8368 (m-80) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1670 time to fit residues: 13.0629 Evaluate side-chains 42 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 121 optimal weight: 20.0000 chunk 295 optimal weight: 6.9990 chunk 290 optimal weight: 9.9990 chunk 212 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 272 optimal weight: 0.0070 chunk 211 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 234 optimal weight: 0.0670 chunk 5 optimal weight: 6.9990 chunk 236 optimal weight: 0.0370 overall best weight: 2.2218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN A 323 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.048049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.041992 restraints weight = 44694.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.043271 restraints weight = 26932.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.044071 restraints weight = 18079.274| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 25620 Z= 0.100 Angle : 0.523 5.154 34792 Z= 0.270 Chirality : 0.041 0.167 3580 Planarity : 0.004 0.046 4452 Dihedral : 4.779 54.682 3492 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.15), residues: 3048 helix: 0.69 (0.14), residues: 1524 sheet: None (None), residues: 0 loop : -2.18 (0.14), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 420 HIS 0.004 0.001 HIS D 308 PHE 0.022 0.001 PHE D 183 TYR 0.008 0.001 TYR A 233 ARG 0.002 0.000 ARG B 678 Details of bonding type rmsd hydrogen bonds : bond 0.03305 ( 916) hydrogen bonds : angle 4.02980 ( 2664) covalent geometry : bond 0.00225 (25620) covalent geometry : angle 0.52341 (34792) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.706 Fit side-chains REVERT: A 159 TYR cc_start: 0.6487 (t80) cc_final: 0.5921 (t80) REVERT: A 270 MET cc_start: 0.8429 (mtp) cc_final: 0.8201 (mtt) REVERT: A 694 TYR cc_start: 0.8781 (m-80) cc_final: 0.8473 (m-80) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1586 time to fit residues: 12.0063 Evaluate side-chains 42 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 187 optimal weight: 7.9990 chunk 210 optimal weight: 3.9990 chunk 135 optimal weight: 10.0000 chunk 173 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 273 optimal weight: 5.9990 chunk 110 optimal weight: 9.9990 chunk 159 optimal weight: 0.1980 chunk 17 optimal weight: 8.9990 chunk 118 optimal weight: 10.0000 chunk 174 optimal weight: 9.9990 overall best weight: 5.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 117 HIS ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN A 485 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.046709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.040781 restraints weight = 44274.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.041965 restraints weight = 26697.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.042779 restraints weight = 17967.796| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25620 Z= 0.152 Angle : 0.565 5.611 34792 Z= 0.293 Chirality : 0.041 0.142 3580 Planarity : 0.004 0.044 4452 Dihedral : 4.663 55.140 3492 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.15), residues: 3048 helix: 0.68 (0.14), residues: 1540 sheet: None (None), residues: 0 loop : -2.09 (0.15), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 209 HIS 0.005 0.001 HIS B 308 PHE 0.017 0.002 PHE D 183 TYR 0.013 0.001 TYR B 360 ARG 0.003 0.000 ARG C 264 Details of bonding type rmsd hydrogen bonds : bond 0.03485 ( 916) hydrogen bonds : angle 4.15178 ( 2664) covalent geometry : bond 0.00341 (25620) covalent geometry : angle 0.56459 (34792) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.664 Fit side-chains REVERT: A 159 TYR cc_start: 0.6447 (t80) cc_final: 0.5866 (t80) REVERT: A 270 MET cc_start: 0.8425 (mtp) cc_final: 0.8221 (mtp) REVERT: A 689 MET cc_start: 0.8609 (mtm) cc_final: 0.8359 (mtp) REVERT: A 694 TYR cc_start: 0.8820 (m-80) cc_final: 0.8517 (m-80) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1575 time to fit residues: 12.5415 Evaluate side-chains 40 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 216 optimal weight: 0.0980 chunk 186 optimal weight: 7.9990 chunk 185 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 227 optimal weight: 0.3980 chunk 31 optimal weight: 8.9990 chunk 190 optimal weight: 10.0000 chunk 39 optimal weight: 0.0970 chunk 236 optimal weight: 0.1980 chunk 209 optimal weight: 6.9990 chunk 11 optimal weight: 0.3980 overall best weight: 0.2378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.048266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.042194 restraints weight = 43246.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.043399 restraints weight = 26439.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.044259 restraints weight = 18072.989| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25620 Z= 0.100 Angle : 0.535 6.116 34792 Z= 0.272 Chirality : 0.041 0.143 3580 Planarity : 0.004 0.046 4452 Dihedral : 4.486 53.794 3492 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.15), residues: 3048 helix: 0.62 (0.14), residues: 1548 sheet: None (None), residues: 0 loop : -2.11 (0.14), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 420 HIS 0.003 0.001 HIS D 308 PHE 0.016 0.001 PHE D 183 TYR 0.018 0.001 TYR C 360 ARG 0.002 0.000 ARG C 678 Details of bonding type rmsd hydrogen bonds : bond 0.02928 ( 916) hydrogen bonds : angle 3.86663 ( 2664) covalent geometry : bond 0.00216 (25620) covalent geometry : angle 0.53457 (34792) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.798 Fit side-chains REVERT: A 159 TYR cc_start: 0.6427 (t80) cc_final: 0.5843 (t80) REVERT: A 270 MET cc_start: 0.8539 (mtp) cc_final: 0.8172 (mtp) REVERT: A 653 ASN cc_start: 0.8748 (m-40) cc_final: 0.8517 (m110) REVERT: A 694 TYR cc_start: 0.8787 (m-80) cc_final: 0.8570 (m-80) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1839 time to fit residues: 15.7252 Evaluate side-chains 42 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 278 optimal weight: 0.9980 chunk 280 optimal weight: 0.0020 chunk 27 optimal weight: 0.2980 chunk 168 optimal weight: 4.9990 chunk 295 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 48 optimal weight: 20.0000 chunk 56 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 264 optimal weight: 10.0000 overall best weight: 1.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN A 357 HIS A 395 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.047734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.041769 restraints weight = 43381.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.043026 restraints weight = 26675.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.043843 restraints weight = 18062.794| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 25620 Z= 0.103 Angle : 0.538 5.347 34792 Z= 0.277 Chirality : 0.041 0.166 3580 Planarity : 0.004 0.048 4452 Dihedral : 4.437 51.822 3492 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.15), residues: 3048 helix: 0.65 (0.14), residues: 1560 sheet: None (None), residues: 0 loop : -2.08 (0.14), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 545 HIS 0.006 0.001 HIS D 357 PHE 0.025 0.002 PHE B 179 TYR 0.010 0.001 TYR A 754 ARG 0.004 0.000 ARG D 757 Details of bonding type rmsd hydrogen bonds : bond 0.03089 ( 916) hydrogen bonds : angle 3.87406 ( 2664) covalent geometry : bond 0.00238 (25620) covalent geometry : angle 0.53839 (34792) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.760 Fit side-chains REVERT: A 159 TYR cc_start: 0.6438 (t80) cc_final: 0.5876 (t80) REVERT: A 270 MET cc_start: 0.8495 (mtp) cc_final: 0.8134 (mtp) REVERT: A 653 ASN cc_start: 0.8784 (m-40) cc_final: 0.8540 (m110) REVERT: A 694 TYR cc_start: 0.8778 (m-80) cc_final: 0.8559 (m-80) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1815 time to fit residues: 13.8352 Evaluate side-chains 40 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 279 optimal weight: 0.0040 chunk 181 optimal weight: 7.9990 chunk 286 optimal weight: 7.9990 chunk 136 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 64 optimal weight: 0.0060 chunk 30 optimal weight: 7.9990 chunk 134 optimal weight: 6.9990 chunk 235 optimal weight: 0.0470 chunk 121 optimal weight: 0.0270 overall best weight: 0.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.048232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.042199 restraints weight = 43520.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.043472 restraints weight = 26491.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.044303 restraints weight = 17841.421| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 25620 Z= 0.100 Angle : 0.560 11.867 34792 Z= 0.281 Chirality : 0.041 0.152 3580 Planarity : 0.005 0.047 4452 Dihedral : 4.343 50.349 3492 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.15), residues: 3048 helix: 0.61 (0.14), residues: 1560 sheet: None (None), residues: 0 loop : -2.10 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 420 HIS 0.010 0.001 HIS A 395 PHE 0.021 0.001 PHE A 179 TYR 0.022 0.001 TYR A 621 ARG 0.002 0.000 ARG C 264 Details of bonding type rmsd hydrogen bonds : bond 0.02963 ( 916) hydrogen bonds : angle 3.82451 ( 2664) covalent geometry : bond 0.00219 (25620) covalent geometry : angle 0.56013 (34792) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.732 Fit side-chains REVERT: A 159 TYR cc_start: 0.6499 (t80) cc_final: 0.5924 (t80) REVERT: A 241 MET cc_start: 0.7344 (tpt) cc_final: 0.6780 (mtm) REVERT: A 270 MET cc_start: 0.8442 (mtp) cc_final: 0.8087 (mtp) REVERT: A 653 ASN cc_start: 0.8731 (m-40) cc_final: 0.8498 (m110) REVERT: A 694 TYR cc_start: 0.8831 (m-80) cc_final: 0.8566 (m-80) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1766 time to fit residues: 12.7262 Evaluate side-chains 41 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 301 optimal weight: 0.0970 chunk 270 optimal weight: 10.0000 chunk 192 optimal weight: 8.9990 chunk 220 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 172 optimal weight: 5.9990 chunk 191 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 273 optimal weight: 0.9990 chunk 146 optimal weight: 0.3980 chunk 70 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.048295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.042205 restraints weight = 44594.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.043458 restraints weight = 27531.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.044313 restraints weight = 18765.398| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 25620 Z= 0.096 Angle : 0.551 10.872 34792 Z= 0.276 Chirality : 0.041 0.142 3580 Planarity : 0.004 0.048 4452 Dihedral : 4.329 49.067 3492 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.15), residues: 3048 helix: 0.69 (0.14), residues: 1556 sheet: None (None), residues: 0 loop : -2.08 (0.14), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 2 HIS 0.006 0.001 HIS B 357 PHE 0.020 0.001 PHE B 183 TYR 0.019 0.001 TYR D 621 ARG 0.001 0.000 ARG C 678 Details of bonding type rmsd hydrogen bonds : bond 0.02905 ( 916) hydrogen bonds : angle 3.81833 ( 2664) covalent geometry : bond 0.00218 (25620) covalent geometry : angle 0.55067 (34792) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.675 Fit side-chains REVERT: A 159 TYR cc_start: 0.6410 (t80) cc_final: 0.5826 (t80) REVERT: A 270 MET cc_start: 0.8455 (mtp) cc_final: 0.8138 (mtp) REVERT: A 653 ASN cc_start: 0.8752 (m-40) cc_final: 0.8514 (m110) REVERT: A 694 TYR cc_start: 0.8838 (m-80) cc_final: 0.8591 (m-80) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1751 time to fit residues: 13.1359 Evaluate side-chains 42 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 208 optimal weight: 4.9990 chunk 270 optimal weight: 9.9990 chunk 39 optimal weight: 0.0050 chunk 73 optimal weight: 9.9990 chunk 119 optimal weight: 0.8980 chunk 146 optimal weight: 0.6980 chunk 251 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 207 optimal weight: 7.9990 chunk 238 optimal weight: 7.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.048428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.042421 restraints weight = 43350.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.043732 restraints weight = 26339.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.044570 restraints weight = 17578.669| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 25620 Z= 0.097 Angle : 0.565 10.030 34792 Z= 0.284 Chirality : 0.041 0.165 3580 Planarity : 0.004 0.047 4452 Dihedral : 4.284 47.961 3492 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.15), residues: 3048 helix: 0.71 (0.14), residues: 1548 sheet: None (None), residues: 0 loop : -2.12 (0.14), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 2 HIS 0.004 0.001 HIS C 357 PHE 0.020 0.001 PHE B 183 TYR 0.030 0.001 TYR D 621 ARG 0.003 0.000 ARG C 103 Details of bonding type rmsd hydrogen bonds : bond 0.02917 ( 916) hydrogen bonds : angle 3.77587 ( 2664) covalent geometry : bond 0.00216 (25620) covalent geometry : angle 0.56486 (34792) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.775 Fit side-chains REVERT: A 159 TYR cc_start: 0.6532 (t80) cc_final: 0.5931 (t80) REVERT: A 241 MET cc_start: 0.7644 (tpt) cc_final: 0.6915 (mtm) REVERT: A 270 MET cc_start: 0.8421 (mtp) cc_final: 0.8104 (mtp) REVERT: A 503 MET cc_start: 0.7862 (mmp) cc_final: 0.7649 (mmm) REVERT: A 653 ASN cc_start: 0.8751 (m-40) cc_final: 0.8503 (m110) REVERT: A 694 TYR cc_start: 0.8848 (m-80) cc_final: 0.8542 (m-80) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1984 time to fit residues: 14.1170 Evaluate side-chains 41 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 175 optimal weight: 1.9990 chunk 176 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 227 optimal weight: 20.0000 chunk 213 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 142 optimal weight: 8.9990 chunk 182 optimal weight: 0.0670 chunk 290 optimal weight: 10.0000 chunk 264 optimal weight: 3.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.048248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.042218 restraints weight = 44460.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.043508 restraints weight = 26955.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.044344 restraints weight = 18136.543| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 25620 Z= 0.099 Angle : 0.552 8.848 34792 Z= 0.279 Chirality : 0.041 0.148 3580 Planarity : 0.004 0.047 4452 Dihedral : 4.246 47.476 3492 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.15), residues: 3048 helix: 0.82 (0.14), residues: 1556 sheet: None (None), residues: 0 loop : -2.03 (0.15), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 420 HIS 0.005 0.001 HIS B 357 PHE 0.020 0.001 PHE C 183 TYR 0.027 0.001 TYR D 621 ARG 0.005 0.000 ARG A 340 Details of bonding type rmsd hydrogen bonds : bond 0.02933 ( 916) hydrogen bonds : angle 3.77466 ( 2664) covalent geometry : bond 0.00229 (25620) covalent geometry : angle 0.55211 (34792) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3837.83 seconds wall clock time: 69 minutes 0.03 seconds (4140.03 seconds total)