Starting phenix.real_space_refine on Mon Aug 25 03:05:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j5z_35996/08_2025/8j5z_35996.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j5z_35996/08_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_35996/08_2025/8j5z_35996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j5z_35996/08_2025/8j5z_35996.map" model { file = "/net/cci-nas-00/data/ceres_data/8j5z_35996/08_2025/8j5z_35996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j5z_35996/08_2025/8j5z_35996.cif" } resolution = 4.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.36, per 1000 atoms: 0.18 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: 1.37 Conformation dependent library (CDL) restraints added in 746.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.46 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: 3.55 Time building geometry restraints manager: 1.80 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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: 0.750 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.470 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.000 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.001 0.000 ARG D 290 TYR 0.005 0.001 TYR D 582 PHE 0.006 0.001 PHE A 183 TRP 0.008 0.001 TRP D 475 HIS 0.002 0.000 HIS C 482 Details of bonding type rmsd covalent geometry : bond 0.00192 (25620) covalent geometry : angle 0.46835 (34792) hydrogen bonds : bond 0.19577 ( 916) hydrogen bonds : angle 5.03690 ( 2664) *********************** 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 : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.6133 (OUTLIER) cc_final: 0.5862 (pp) REVERT: A 27 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7334 (tpt90) REVERT: A 159 TYR cc_start: 0.6414 (t80) cc_final: 0.5664 (t80) REVERT: A 193 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8386 (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: 0.7164 (p90) REVERT: A 413 GLN cc_start: 0.7463 (tt0) cc_final: 0.7047 (tt0) REVERT: A 466 MET cc_start: 0.7962 (mmt) cc_final: 0.7598 (tpt) REVERT: A 485 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7470 (mt0) REVERT: A 486 LEU cc_start: 0.8513 (tp) cc_final: 0.8307 (tt) outliers start: 26 outliers final: 7 residues processed: 123 average time/residue: 0.0955 time to fit residues: 14.6379 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 : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 197 optimal weight: 0.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.0570 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 2.9990 overall best weight: 0.9104 ------------------------------------------------------------------------------- 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 = 0.049987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.043597 restraints weight = 43287.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.044933 restraints weight = 26793.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.045808 restraints weight = 18178.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.046470 restraints weight = 13243.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.046917 restraints weight = 10182.397| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25620 Z= 0.120 Angle : 0.581 7.250 34792 Z= 0.298 Chirality : 0.042 0.216 3580 Planarity : 0.005 0.047 4452 Dihedral : 8.839 77.785 3492 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.15), residues: 3048 helix: 0.66 (0.14), residues: 1492 sheet: None (None), residues: 0 loop : -2.12 (0.15), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 340 TYR 0.024 0.001 TYR A 360 PHE 0.021 0.002 PHE B 183 TRP 0.024 0.001 TRP D 30 HIS 0.008 0.001 HIS C 299 Details of bonding type rmsd covalent geometry : bond 0.00255 (25620) covalent geometry : angle 0.58092 (34792) hydrogen bonds : bond 0.04496 ( 916) hydrogen bonds : angle 4.28123 ( 2664) *********************** 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 : 0.184 Fit side-chains revert: symmetry clash REVERT: A 159 TYR cc_start: 0.6625 (t80) cc_final: 0.6268 (t80) REVERT: A 230 LEU cc_start: 0.9070 (mm) cc_final: 0.8805 (mt) REVERT: A 270 MET cc_start: 0.8120 (mtp) cc_final: 0.7856 (mtp) REVERT: A 413 GLN cc_start: 0.7356 (tt0) cc_final: 0.7125 (tt0) REVERT: A 466 MET cc_start: 0.7707 (mmt) cc_final: 0.7362 (tpt) REVERT: A 499 LEU cc_start: 0.7920 (pp) cc_final: 0.7603 (pp) REVERT: A 694 TYR cc_start: 0.8820 (m-80) cc_final: 0.8403 (m-80) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.0713 time to fit residues: 6.5103 Evaluate side-chains 45 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 49 optimal weight: 10.0000 chunk 170 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 chunk 229 optimal weight: 5.9990 chunk 230 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 243 optimal weight: 3.9990 chunk 134 optimal weight: 20.0000 chunk 245 optimal weight: 0.5980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN A 485 GLN A 562 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 = 0.3058 r_free = 0.3058 target = 0.048142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.042125 restraints weight = 45066.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.043392 restraints weight = 27315.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.044268 restraints weight = 18305.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.044894 restraints weight = 13234.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.045373 restraints weight = 10127.912| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25620 Z= 0.112 Angle : 0.550 7.756 34792 Z= 0.277 Chirality : 0.041 0.183 3580 Planarity : 0.004 0.047 4452 Dihedral : 6.119 57.404 3492 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.15), residues: 3048 helix: 0.74 (0.14), residues: 1524 sheet: None (None), residues: 0 loop : -2.10 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 27 TYR 0.015 0.001 TYR D 360 PHE 0.023 0.001 PHE D 183 TRP 0.021 0.001 TRP A 30 HIS 0.008 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00252 (25620) covalent geometry : angle 0.54998 (34792) hydrogen bonds : bond 0.03562 ( 916) hydrogen bonds : angle 4.10131 ( 2664) *********************** 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 : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 TYR cc_start: 0.6589 (t80) cc_final: 0.5942 (t80) REVERT: A 694 TYR cc_start: 0.8793 (m-80) cc_final: 0.8384 (m-80) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0558 time to fit residues: 4.2912 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 : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 27 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 163 optimal weight: 20.0000 chunk 171 optimal weight: 0.0050 chunk 157 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 14 optimal weight: 0.0470 chunk 123 optimal weight: 0.0050 chunk 46 optimal weight: 0.0000 chunk 150 optimal weight: 6.9990 overall best weight: 0.2112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3114 r_free = 0.3114 target = 0.049753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.043471 restraints weight = 43212.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.044778 restraints weight = 26130.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.045627 restraints weight = 17522.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.046223 restraints weight = 12715.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.046711 restraints weight = 9867.539| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 25620 Z= 0.096 Angle : 0.510 5.752 34792 Z= 0.260 Chirality : 0.040 0.167 3580 Planarity : 0.004 0.047 4452 Dihedral : 4.452 48.976 3492 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.15), residues: 3048 helix: 0.62 (0.14), residues: 1532 sheet: None (None), residues: 0 loop : -2.16 (0.14), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 264 TYR 0.009 0.001 TYR B 233 PHE 0.013 0.001 PHE D 183 TRP 0.017 0.001 TRP D 420 HIS 0.003 0.000 HIS C 357 Details of bonding type rmsd covalent geometry : bond 0.00199 (25620) covalent geometry : angle 0.50966 (34792) hydrogen bonds : bond 0.03142 ( 916) hydrogen bonds : angle 3.92040 ( 2664) *********************** 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 56 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: A 159 TYR cc_start: 0.6616 (t80) cc_final: 0.6266 (t80) REVERT: A 219 MET cc_start: 0.8323 (ptm) cc_final: 0.8107 (ttp) REVERT: A 270 MET cc_start: 0.8460 (mtp) cc_final: 0.8231 (mtp) REVERT: A 546 MET cc_start: 0.8216 (mmt) cc_final: 0.7974 (mmt) REVERT: A 694 TYR cc_start: 0.8812 (m-80) cc_final: 0.8451 (m-80) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.0590 time to fit residues: 4.7871 Evaluate side-chains 43 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 52 optimal weight: 0.0000 chunk 158 optimal weight: 0.0470 chunk 20 optimal weight: 0.0870 chunk 44 optimal weight: 0.6980 chunk 268 optimal weight: 6.9990 chunk 249 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 184 optimal weight: 7.9990 chunk 289 optimal weight: 0.0010 chunk 297 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.1666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3100 r_free = 0.3100 target = 0.049296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.043223 restraints weight = 45500.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.044512 restraints weight = 27303.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.045391 restraints weight = 18303.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.046012 restraints weight = 13171.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.046486 restraints weight = 10116.055| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 25620 Z= 0.092 Angle : 0.508 6.001 34792 Z= 0.258 Chirality : 0.040 0.167 3580 Planarity : 0.004 0.047 4452 Dihedral : 4.247 51.486 3492 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.15), residues: 3048 helix: 0.61 (0.14), residues: 1544 sheet: None (None), residues: 0 loop : -2.11 (0.14), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 678 TYR 0.009 0.001 TYR B 621 PHE 0.024 0.001 PHE A 179 TRP 0.035 0.001 TRP D 209 HIS 0.006 0.001 HIS D 357 Details of bonding type rmsd covalent geometry : bond 0.00194 (25620) covalent geometry : angle 0.50787 (34792) hydrogen bonds : bond 0.02911 ( 916) hydrogen bonds : angle 3.85040 ( 2664) *********************** 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 54 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: A 159 TYR cc_start: 0.6591 (t80) cc_final: 0.6251 (t80) REVERT: A 241 MET cc_start: 0.7255 (tpt) cc_final: 0.6661 (mtm) REVERT: A 653 ASN cc_start: 0.8744 (m-40) cc_final: 0.8480 (m110) REVERT: A 694 TYR cc_start: 0.8786 (m-80) cc_final: 0.8524 (m-80) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0474 time to fit residues: 3.7599 Evaluate side-chains 43 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 3 optimal weight: 10.0000 chunk 45 optimal weight: 0.0010 chunk 82 optimal weight: 8.9990 chunk 41 optimal weight: 0.2980 chunk 105 optimal weight: 0.5980 chunk 58 optimal weight: 7.9990 chunk 195 optimal weight: 7.9990 chunk 217 optimal weight: 0.3980 chunk 34 optimal weight: 9.9990 chunk 301 optimal weight: 0.0770 chunk 192 optimal weight: 1.9990 overall best weight: 0.2744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3108 r_free = 0.3108 target = 0.049672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.043588 restraints weight = 44225.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.044905 restraints weight = 27165.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.045751 restraints weight = 18254.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.046391 restraints weight = 13252.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.046878 restraints weight = 10167.065| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 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 : 0.002 0.027 25620 Z= 0.095 Angle : 0.514 6.311 34792 Z= 0.258 Chirality : 0.040 0.149 3580 Planarity : 0.004 0.050 4452 Dihedral : 4.165 49.598 3492 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.15), residues: 3048 helix: 0.59 (0.14), residues: 1552 sheet: None (None), residues: 0 loop : -2.06 (0.14), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 678 TYR 0.017 0.001 TYR B 360 PHE 0.018 0.001 PHE A 179 TRP 0.015 0.001 TRP A 420 HIS 0.002 0.000 HIS B 255 Details of bonding type rmsd covalent geometry : bond 0.00202 (25620) covalent geometry : angle 0.51429 (34792) hydrogen bonds : bond 0.02858 ( 916) hydrogen bonds : angle 3.79854 ( 2664) *********************** 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 : 0.150 Fit side-chains revert: symmetry clash REVERT: A 159 TYR cc_start: 0.6570 (t80) cc_final: 0.6192 (t80) REVERT: A 241 MET cc_start: 0.7277 (tpt) cc_final: 0.6653 (mtm) REVERT: A 413 GLN cc_start: 0.7310 (tt0) cc_final: 0.7059 (tt0) REVERT: A 486 LEU cc_start: 0.7880 (tp) cc_final: 0.7511 (tp) REVERT: A 552 MET cc_start: 0.6051 (mmm) cc_final: 0.5699 (mmm) REVERT: A 653 ASN cc_start: 0.8716 (m-40) cc_final: 0.8463 (m110) REVERT: A 689 MET cc_start: 0.8567 (mtm) cc_final: 0.8225 (mtp) REVERT: A 694 TYR cc_start: 0.8713 (m-80) cc_final: 0.8491 (m-80) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.0482 time to fit residues: 4.1902 Evaluate side-chains 45 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 122 optimal weight: 0.8980 chunk 229 optimal weight: 0.0060 chunk 285 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 121 optimal weight: 0.4980 chunk 258 optimal weight: 5.9990 chunk 226 optimal weight: 0.8980 chunk 44 optimal weight: 0.2980 chunk 268 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- 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 427 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 = 0.3114 r_free = 0.3114 target = 0.049789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.043683 restraints weight = 44026.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.044971 restraints weight = 26824.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.045819 restraints weight = 18070.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.046428 restraints weight = 13140.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.046883 restraints weight = 10110.179| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 25620 Z= 0.090 Angle : 0.512 6.130 34792 Z= 0.257 Chirality : 0.040 0.162 3580 Planarity : 0.004 0.048 4452 Dihedral : 4.059 47.727 3492 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.15), residues: 3048 helix: 0.69 (0.14), residues: 1552 sheet: None (None), residues: 0 loop : -2.03 (0.14), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 669 TYR 0.018 0.001 TYR C 360 PHE 0.030 0.001 PHE A 619 TRP 0.015 0.001 TRP D 545 HIS 0.002 0.000 HIS B 255 Details of bonding type rmsd covalent geometry : bond 0.00194 (25620) covalent geometry : angle 0.51196 (34792) hydrogen bonds : bond 0.02758 ( 916) hydrogen bonds : angle 3.75644 ( 2664) *********************** 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 61 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: A 159 TYR cc_start: 0.6624 (t80) cc_final: 0.6209 (t80) REVERT: A 241 MET cc_start: 0.7278 (tpt) cc_final: 0.6648 (mtm) REVERT: A 486 LEU cc_start: 0.7855 (tp) cc_final: 0.7475 (tp) REVERT: A 653 ASN cc_start: 0.8721 (m-40) cc_final: 0.8470 (m110) REVERT: A 694 TYR cc_start: 0.8770 (m-80) cc_final: 0.8515 (m-80) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0610 time to fit residues: 5.3962 Evaluate side-chains 45 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 21 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 121 optimal weight: 0.0970 chunk 150 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 98 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 272 optimal weight: 6.9990 chunk 173 optimal weight: 9.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN A 323 GLN A 357 HIS A 596 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.049158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.043070 restraints weight = 44721.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.044369 restraints weight = 27174.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.045219 restraints weight = 18151.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.045874 restraints weight = 13123.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.046237 restraints weight = 9997.258| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 25620 Z= 0.103 Angle : 0.522 5.097 34792 Z= 0.266 Chirality : 0.041 0.170 3580 Planarity : 0.004 0.047 4452 Dihedral : 4.088 47.792 3492 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.15), residues: 3048 helix: 0.82 (0.14), residues: 1552 sheet: None (None), residues: 0 loop : -2.05 (0.14), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 340 TYR 0.014 0.001 TYR C 621 PHE 0.023 0.002 PHE D 619 TRP 0.016 0.001 TRP A 67 HIS 0.003 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00234 (25620) covalent geometry : angle 0.52193 (34792) hydrogen bonds : bond 0.02857 ( 916) hydrogen bonds : angle 3.81809 ( 2664) *********************** 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 52 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 TYR cc_start: 0.6578 (t80) cc_final: 0.6201 (t80) REVERT: A 466 MET cc_start: 0.7112 (mmm) cc_final: 0.6536 (tmm) REVERT: A 486 LEU cc_start: 0.7919 (tp) cc_final: 0.7693 (tp) REVERT: A 694 TYR cc_start: 0.8859 (m-80) cc_final: 0.8532 (m-80) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0513 time to fit residues: 3.8368 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 : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 132 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 216 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 211 optimal weight: 3.9990 chunk 78 optimal weight: 30.0000 chunk 240 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 171 optimal weight: 6.9990 chunk 288 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 = 0.3090 r_free = 0.3090 target = 0.048833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.042770 restraints weight = 45410.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.044036 restraints weight = 27968.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.044846 restraints weight = 18972.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.045422 restraints weight = 13802.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.045870 restraints weight = 10852.875| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3968 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 : 0.537 7.231 34792 Z= 0.273 Chirality : 0.041 0.175 3580 Planarity : 0.004 0.047 4452 Dihedral : 4.181 48.799 3492 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.15), residues: 3048 helix: 0.88 (0.14), residues: 1548 sheet: None (None), residues: 0 loop : -2.07 (0.14), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 340 TYR 0.013 0.001 TYR D 621 PHE 0.019 0.001 PHE A 424 TRP 0.022 0.001 TRP B 67 HIS 0.002 0.001 HIS C 308 Details of bonding type rmsd covalent geometry : bond 0.00230 (25620) covalent geometry : angle 0.53674 (34792) hydrogen bonds : bond 0.02758 ( 916) hydrogen bonds : angle 3.81615 ( 2664) *********************** 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 55 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.172 Fit side-chains REVERT: A 159 TYR cc_start: 0.6564 (t80) cc_final: 0.6174 (t80) REVERT: A 251 TYR cc_start: 0.7290 (m-80) cc_final: 0.6845 (m-80) REVERT: A 486 LEU cc_start: 0.7882 (tp) cc_final: 0.7633 (tp) REVERT: A 694 TYR cc_start: 0.8823 (m-80) cc_final: 0.8545 (m-80) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0459 time to fit residues: 3.6830 Evaluate side-chains 47 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 73 optimal weight: 10.0000 chunk 189 optimal weight: 0.0870 chunk 150 optimal weight: 7.9990 chunk 271 optimal weight: 0.0370 chunk 75 optimal weight: 8.9990 chunk 246 optimal weight: 8.9990 chunk 273 optimal weight: 0.0980 chunk 225 optimal weight: 7.9990 chunk 241 optimal weight: 3.9990 chunk 171 optimal weight: 0.2980 chunk 230 optimal weight: 20.0000 overall best weight: 0.9038 ------------------------------------------------------------------------------- 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 = 0.3110 r_free = 0.3110 target = 0.049502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.043453 restraints weight = 44046.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.044757 restraints weight = 26798.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.045599 restraints weight = 18008.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.046236 restraints weight = 13037.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.046696 restraints weight = 9985.998| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.4136 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 : 0.558 7.450 34792 Z= 0.283 Chirality : 0.041 0.177 3580 Planarity : 0.005 0.048 4452 Dihedral : 4.178 48.426 3492 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.15), residues: 3048 helix: 0.82 (0.14), residues: 1548 sheet: None (None), residues: 0 loop : -2.03 (0.14), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 669 TYR 0.032 0.001 TYR B 621 PHE 0.022 0.001 PHE A 179 TRP 0.022 0.001 TRP D 67 HIS 0.003 0.000 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00217 (25620) covalent geometry : angle 0.55799 (34792) hydrogen bonds : bond 0.02899 ( 916) hydrogen bonds : angle 3.80040 ( 2664) ********************** 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 61 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.228 Fit side-chains REVERT: A 159 TYR cc_start: 0.6541 (t80) cc_final: 0.6152 (t80) REVERT: A 486 LEU cc_start: 0.7897 (tp) cc_final: 0.7629 (tp) REVERT: A 653 ASN cc_start: 0.8698 (m-40) cc_final: 0.8429 (m110) REVERT: A 694 TYR cc_start: 0.8843 (m-80) cc_final: 0.8519 (m-80) REVERT: A 736 MET cc_start: 0.8526 (mmt) cc_final: 0.8159 (mmm) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0547 time to fit residues: 4.8219 Evaluate side-chains 49 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 207 optimal weight: 3.9990 chunk 184 optimal weight: 8.9990 chunk 213 optimal weight: 0.9980 chunk 99 optimal weight: 0.0670 chunk 294 optimal weight: 8.9990 chunk 120 optimal weight: 4.9990 chunk 2 optimal weight: 30.0000 chunk 153 optimal weight: 8.9990 chunk 214 optimal weight: 9.9990 chunk 200 optimal weight: 9.9990 chunk 174 optimal weight: 7.9990 overall best weight: 3.6124 ------------------------------------------------------------------------------- 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 = 0.3067 r_free = 0.3067 target = 0.047952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.042047 restraints weight = 45222.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.043290 restraints weight = 27953.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.044098 restraints weight = 18947.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.044728 restraints weight = 13852.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.045190 restraints weight = 10631.093| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25620 Z= 0.124 Angle : 0.585 7.694 34792 Z= 0.299 Chirality : 0.042 0.170 3580 Planarity : 0.005 0.053 4452 Dihedral : 4.285 48.777 3492 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.15), residues: 3048 helix: 0.82 (0.14), residues: 1548 sheet: None (None), residues: 0 loop : -2.05 (0.14), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 707 TYR 0.016 0.001 TYR D 621 PHE 0.023 0.002 PHE B 183 TRP 0.022 0.001 TRP B 67 HIS 0.003 0.001 HIS A 308 Details of bonding type rmsd covalent geometry : bond 0.00280 (25620) covalent geometry : angle 0.58505 (34792) hydrogen bonds : bond 0.03134 ( 916) hydrogen bonds : angle 3.99198 ( 2664) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1396.89 seconds wall clock time: 25 minutes 54.41 seconds (1554.41 seconds total)