Starting phenix.real_space_refine on Sun Jul 5 01:54:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8j5z_35996/07_2026/8j5z_35996.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j5z_35996/07_2026/8j5z_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8j5z_35996/07_2026/8j5z_35996.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8j5z_35996/07_2026/8j5z_35996.cif" model { file = "/net/cci-nas-00/data/ceres_data/8j5z_35996/07_2026/8j5z_35996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j5z_35996/07_2026/8j5z_35996.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j5z_35996/07_2026/8j5z_35996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j5z_35996/07_2026/8j5z_35996.map" } 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-dev-6108/lib/python3.11/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: 4.61, per 1000 atoms: 0.19 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: 2.34 Conformation dependent library (CDL) restraints added in 676.8 milliseconds 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: 0.51 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: 3.79 Time building geometry restraints manager: 3.00 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 - 15.95: 14127 15.95 - 31.91: 622 31.91 - 47.86: 142 47.86 - 63.81: 73 63.81 - 79.77: 8 Dihedral angle restraints: 14972 sinusoidal: 6104 harmonic: 8868 Sorted by residual: dihedral pdb=" N LEU C 555 " pdb=" CA LEU C 555 " pdb=" CB LEU C 555 " pdb=" CG LEU C 555 " ideal model delta sinusoidal sigma weight residual -180.00 -121.16 -58.84 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N LEU D 555 " pdb=" CA LEU D 555 " pdb=" CB LEU D 555 " pdb=" CG LEU D 555 " ideal model delta sinusoidal sigma weight residual -180.00 -121.17 -58.83 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N LEU B 555 " pdb=" CA LEU B 555 " pdb=" CB LEU B 555 " pdb=" CG LEU B 555 " ideal model delta sinusoidal sigma weight residual -180.00 -121.21 -58.79 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 14969 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: 0.870 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: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 18.420 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 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 : 10.492 79.766 9316 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 are 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/Z covalent geometry : bond 0.00192 / 0.10 (25620) covalent geometry : angle 0.46835 / 0.24 (34792) hydrogen bonds : bond 0.19577 / 12.52 ( 916) hydrogen bonds : angle 5.03690 / 3.53 ( 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 : 0.154 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: 0.7624 (OUTLIER) cc_final: 0.7334 (tpt90) REVERT: A 159 TYR cc_start: 0.6414 (t80) cc_final: 0.5665 (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: 0.0916 time to fit residues: 14.1356 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 : 0.233 ------------------------------------------------------------------------------- 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... A 11 ASN A 323 GLN ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 480 GLN ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 ASN ** A 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.050104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.043688 restraints weight = 43912.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.045035 restraints weight = 27482.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.045912 restraints weight = 18731.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.046563 restraints weight = 13718.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.047021 restraints weight = 10592.576| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2685 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= 0.122 Angle : 0.574 6.402 34792 Z= 0.299 Chirality : 0.042 0.196 3580 Planarity : 0.005 0.049 4452 Dihedral : 3.990 48.259 3396 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 are not related in a simple way. whole: -1.01 (0.15), residues: 3048 helix: 0.69 (0.14), residues: 1480 sheet: None (None), residues: 0 loop : -2.12 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 645 TYR 0.017 0.001 TYR D 360 PHE 0.021 0.002 PHE A 183 TRP 0.023 0.001 TRP B 30 HIS 0.007 0.001 HIS C 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (25620) covalent geometry : angle 0.57420 / 0.30 (34792) hydrogen bonds : bond 0.04489 / 2.93 ( 916) hydrogen bonds : angle 4.32741 / 3.04 ( 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 : 0.172 Fit side-chains revert: symmetry clash REVERT: A 159 TYR cc_start: 0.6627 (t80) cc_final: 0.6269 (t80) REVERT: A 230 LEU cc_start: 0.9076 (mm) cc_final: 0.8866 (mt) REVERT: A 270 MET cc_start: 0.8095 (mtp) cc_final: 0.7816 (mtp) REVERT: A 413 GLN cc_start: 0.7340 (tt0) cc_final: 0.7117 (tt0) REVERT: A 466 MET cc_start: 0.7679 (mmt) cc_final: 0.7328 (tpt) REVERT: A 499 LEU cc_start: 0.7940 (pp) cc_final: 0.7607 (pp) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.0764 time to fit residues: 6.9589 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 : 0.231 ------------------------------------------------------------------------------- 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: 6.9990 chunk 170 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 chunk 151 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 229 optimal weight: 0.1980 chunk 230 optimal weight: 8.9990 chunk 103 optimal weight: 0.0070 chunk 243 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 245 optimal weight: 5.9990 overall best weight: 1.2402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 323 GLN A 469 HIS A 485 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.048867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.042862 restraints weight = 44522.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.044120 restraints weight = 26980.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.044979 restraints weight = 18128.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.045634 restraints weight = 13165.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.046082 restraints weight = 10077.029| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25620 Z= 0.102 Angle : 0.532 7.013 34792 Z= 0.271 Chirality : 0.041 0.176 3580 Planarity : 0.004 0.046 4452 Dihedral : 3.983 48.697 3396 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % 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 are not related in a simple way. whole: -0.98 (0.15), residues: 3048 helix: 0.68 (0.14), residues: 1500 sheet: None (None), residues: 0 loop : -2.11 (0.14), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 27 TYR 0.013 0.001 TYR B 360 PHE 0.013 0.001 PHE A 183 TRP 0.017 0.001 TRP C 30 HIS 0.006 0.001 HIS D 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (25620) covalent geometry : angle 0.53193 / 0.27 (34792) hydrogen bonds : bond 0.03578 / 2.33 ( 916) hydrogen bonds : angle 4.11135 / 2.90 ( 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 57 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 159 TYR cc_start: 0.6551 (t80) cc_final: 0.6195 (t80) REVERT: A 413 GLN cc_start: 0.7277 (tt0) cc_final: 0.7008 (tt0) REVERT: A 694 TYR cc_start: 0.8818 (m-80) cc_final: 0.8390 (m-80) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.0614 time to fit residues: 5.1026 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 : 0.197 ------------------------------------------------------------------------------- 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: 0.0170 chunk 32 optimal weight: 6.9990 chunk 163 optimal weight: 20.0000 chunk 171 optimal weight: 0.0770 chunk 157 optimal weight: 9.9990 chunk 84 optimal weight: 30.0000 chunk 65 optimal weight: 0.0570 chunk 14 optimal weight: 3.9990 chunk 123 optimal weight: 0.2980 chunk 46 optimal weight: 9.9990 chunk 150 optimal weight: 1.9990 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3112 r_free = 0.3112 target = 0.049683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.043430 restraints weight = 43552.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.044714 restraints weight = 26342.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.045582 restraints weight = 17724.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.046212 restraints weight = 12886.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.046718 restraints weight = 9886.172| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3260 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 : 0.515 5.772 34792 Z= 0.263 Chirality : 0.041 0.168 3580 Planarity : 0.004 0.047 4452 Dihedral : 3.905 47.496 3396 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % 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 are not related in a simple way. whole: -1.02 (0.15), residues: 3048 helix: 0.66 (0.14), residues: 1528 sheet: None (None), residues: 0 loop : -2.18 (0.14), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 264 TYR 0.011 0.001 TYR A 360 PHE 0.020 0.001 PHE D 179 TRP 0.014 0.001 TRP B 420 HIS 0.003 0.000 HIS C 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.10 (25620) covalent geometry : angle 0.51511 / 0.26 (34792) hydrogen bonds : bond 0.03235 / 2.11 ( 916) hydrogen bonds : angle 3.94836 / 2.78 ( 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 58 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 159 TYR cc_start: 0.6600 (t80) cc_final: 0.6251 (t80) REVERT: A 219 MET cc_start: 0.8253 (ptm) cc_final: 0.8046 (ttp) REVERT: A 241 MET cc_start: 0.7669 (tpt) cc_final: 0.6792 (mtm) REVERT: A 413 GLN cc_start: 0.7263 (tt0) cc_final: 0.7023 (tt0) REVERT: A 546 MET cc_start: 0.8230 (mmt) cc_final: 0.7985 (mmt) REVERT: A 694 TYR cc_start: 0.8822 (m-80) cc_final: 0.8442 (m-80) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.0563 time to fit residues: 4.7689 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 : 0.240 ------------------------------------------------------------------------------- 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: 8.9990 chunk 158 optimal weight: 5.9990 chunk 20 optimal weight: 0.3980 chunk 44 optimal weight: 6.9990 chunk 268 optimal weight: 20.0000 chunk 249 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 184 optimal weight: 10.0000 chunk 289 optimal weight: 4.9990 chunk 297 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 overall best weight: 5.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN A 323 GLN A 596 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.046507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.040552 restraints weight = 45970.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.041781 restraints weight = 27774.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.042589 restraints weight = 18732.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.043130 restraints weight = 13608.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.043637 restraints weight = 10670.828| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3544 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= 0.152 Angle : 0.558 5.461 34792 Z= 0.286 Chirality : 0.041 0.169 3580 Planarity : 0.004 0.046 4452 Dihedral : 4.114 50.278 3396 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.15), residues: 3048 helix: 0.78 (0.14), residues: 1536 sheet: None (None), residues: 0 loop : -2.11 (0.14), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 707 TYR 0.014 0.001 TYR D 360 PHE 0.020 0.002 PHE D 183 TRP 0.033 0.002 TRP D 209 HIS 0.004 0.001 HIS C 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (25620) covalent geometry : angle 0.55756 / 0.29 (34792) hydrogen bonds : bond 0.03302 / 2.11 ( 916) hydrogen bonds : angle 4.10583 / 2.89 ( 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 52 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.224 Fit side-chains REVERT: A 159 TYR cc_start: 0.6426 (t80) cc_final: 0.5772 (t80) REVERT: A 241 MET cc_start: 0.7696 (tpt) cc_final: 0.6658 (mtm) REVERT: A 270 MET cc_start: 0.8421 (mtp) cc_final: 0.8048 (mtp) REVERT: A 466 MET cc_start: 0.7265 (mmt) cc_final: 0.6850 (tpt) REVERT: A 694 TYR cc_start: 0.8808 (m-80) cc_final: 0.8440 (m-80) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0606 time to fit residues: 4.6287 Evaluate side-chains 40 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.194 ------------------------------------------------------------------------------- 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: 9.9990 chunk 45 optimal weight: 0.0470 chunk 82 optimal weight: 0.0270 chunk 41 optimal weight: 1.9990 chunk 105 optimal weight: 0.0870 chunk 58 optimal weight: 8.9990 chunk 195 optimal weight: 0.0060 chunk 217 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 301 optimal weight: 7.9990 chunk 192 optimal weight: 8.9990 overall best weight: 0.4332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3073 r_free = 0.3073 target = 0.048289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.042253 restraints weight = 43672.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.043492 restraints weight = 26766.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.044282 restraints weight = 18102.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.044925 restraints weight = 13245.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.045307 restraints weight = 10194.664| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3609 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 : 0.524 6.063 34792 Z= 0.264 Chirality : 0.040 0.134 3580 Planarity : 0.004 0.046 4452 Dihedral : 3.934 48.637 3396 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % 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 are not related in a simple way. whole: -0.87 (0.15), residues: 3048 helix: 0.77 (0.14), residues: 1528 sheet: None (None), residues: 0 loop : -2.10 (0.14), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 156 TYR 0.014 0.001 TYR C 360 PHE 0.013 0.001 PHE D 183 TRP 0.022 0.001 TRP C 246 HIS 0.004 0.001 HIS B 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.09 (25620) covalent geometry : angle 0.52449 / 0.26 (34792) hydrogen bonds : bond 0.02971 / 1.93 ( 916) hydrogen bonds : angle 3.78641 / 2.67 ( 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 53 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.247 Fit side-chains REVERT: A 159 TYR cc_start: 0.6560 (t80) cc_final: 0.5902 (t80) REVERT: A 546 MET cc_start: 0.8166 (mmt) cc_final: 0.7889 (mmt) REVERT: A 653 ASN cc_start: 0.8755 (m-40) cc_final: 0.8499 (m110) REVERT: A 694 TYR cc_start: 0.8804 (m-80) cc_final: 0.8559 (m-80) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.0532 time to fit residues: 4.1732 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 : 0.222 ------------------------------------------------------------------------------- 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: 10.0000 chunk 229 optimal weight: 0.0040 chunk 285 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 121 optimal weight: 6.9990 chunk 258 optimal weight: 20.0000 chunk 226 optimal weight: 0.0060 chunk 44 optimal weight: 0.7980 chunk 268 optimal weight: 0.6980 chunk 118 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.4808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN A 357 HIS A 395 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.048818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.042813 restraints weight = 43809.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.044058 restraints weight = 26746.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.044856 restraints weight = 18034.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.045490 restraints weight = 13301.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.045963 restraints weight = 10237.303| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25620 Z= 0.104 Angle : 0.561 11.059 34792 Z= 0.279 Chirality : 0.041 0.167 3580 Planarity : 0.004 0.049 4452 Dihedral : 3.962 48.757 3396 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % 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 are not related in a simple way. whole: -0.93 (0.15), residues: 3048 helix: 0.68 (0.14), residues: 1536 sheet: None (None), residues: 0 loop : -2.09 (0.14), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 757 TYR 0.010 0.001 TYR C 754 PHE 0.021 0.001 PHE C 179 TRP 0.018 0.001 TRP D 222 HIS 0.003 0.000 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (25620) covalent geometry : angle 0.56075 / 0.28 (34792) hydrogen bonds : bond 0.02969 / 1.92 ( 916) hydrogen bonds : angle 3.82308 / 2.71 ( 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 54 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 159 TYR cc_start: 0.6490 (t80) cc_final: 0.6144 (t80) REVERT: A 653 ASN cc_start: 0.8736 (m-40) cc_final: 0.8480 (m110) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0750 time to fit residues: 5.7339 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 : 0.241 ------------------------------------------------------------------------------- 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: 0.0470 chunk 66 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 121 optimal weight: 8.9990 chunk 150 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 98 optimal weight: 0.0470 chunk 38 optimal weight: 5.9990 chunk 272 optimal weight: 9.9990 chunk 173 optimal weight: 9.9990 overall best weight: 1.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN A 395 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.048239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.042274 restraints weight = 45288.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.043504 restraints weight = 27577.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.044344 restraints weight = 18623.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.044962 restraints weight = 13465.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.045449 restraints weight = 10320.258| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3914 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= 0.095 Angle : 0.537 9.470 34792 Z= 0.269 Chirality : 0.040 0.157 3580 Planarity : 0.004 0.047 4452 Dihedral : 3.950 47.253 3396 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % 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 are not related in a simple way. whole: -0.89 (0.15), residues: 3048 helix: 0.71 (0.14), residues: 1544 sheet: None (None), residues: 0 loop : -2.09 (0.15), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 264 TYR 0.013 0.001 TYR B 621 PHE 0.019 0.001 PHE B 183 TRP 0.021 0.001 TRP A 2 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (25620) covalent geometry : angle 0.53692 / 0.27 (34792) hydrogen bonds : bond 0.02803 / 1.80 ( 916) hydrogen bonds : angle 3.84034 / 2.72 ( 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 57 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.246 Fit side-chains REVERT: A 159 TYR cc_start: 0.6501 (t80) cc_final: 0.5868 (t80) REVERT: A 378 CYS cc_start: 0.8484 (t) cc_final: 0.8133 (t) REVERT: A 466 MET cc_start: 0.7108 (tpp) cc_final: 0.6787 (tpt) REVERT: A 653 ASN cc_start: 0.8765 (m-40) cc_final: 0.8511 (m110) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.0655 time to fit residues: 5.2558 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 : 0.210 ------------------------------------------------------------------------------- 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: 0.7980 chunk 107 optimal weight: 0.0970 chunk 92 optimal weight: 9.9990 chunk 216 optimal weight: 0.9980 chunk 9 optimal weight: 20.0000 chunk 211 optimal weight: 2.9990 chunk 78 optimal weight: 0.2980 chunk 240 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 171 optimal weight: 6.9990 chunk 288 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3088 r_free = 0.3088 target = 0.048712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.042835 restraints weight = 45375.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.044096 restraints weight = 27582.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.044921 restraints weight = 18461.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.045546 restraints weight = 13262.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.046029 restraints weight = 10121.404| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 25620 Z= 0.097 Angle : 0.563 9.430 34792 Z= 0.283 Chirality : 0.041 0.156 3580 Planarity : 0.005 0.068 4452 Dihedral : 3.896 45.594 3396 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.19 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 are not related in a simple way. whole: -0.86 (0.15), residues: 3048 helix: 0.76 (0.14), residues: 1540 sheet: None (None), residues: 0 loop : -2.10 (0.14), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 669 TYR 0.032 0.001 TYR B 621 PHE 0.023 0.001 PHE B 424 TRP 0.019 0.001 TRP A 545 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (25620) covalent geometry : angle 0.56306 / 0.28 (34792) hydrogen bonds : bond 0.02769 / 1.76 ( 916) hydrogen bonds : angle 3.81985 / 2.72 ( 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 62 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.158 Fit side-chains REVERT: A 159 TYR cc_start: 0.6588 (t80) cc_final: 0.6220 (t80) REVERT: A 251 TYR cc_start: 0.7237 (m-80) cc_final: 0.6863 (m-80) REVERT: A 270 MET cc_start: 0.8658 (mtp) cc_final: 0.8421 (mtp) REVERT: A 486 LEU cc_start: 0.7958 (tp) cc_final: 0.7730 (tp) REVERT: A 653 ASN cc_start: 0.8744 (m-40) cc_final: 0.8498 (m110) REVERT: A 694 TYR cc_start: 0.8752 (m-80) cc_final: 0.8522 (m-80) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0698 time to fit residues: 5.9901 Evaluate side-chains 48 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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: 7.9990 chunk 189 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 271 optimal weight: 0.3980 chunk 75 optimal weight: 7.9990 chunk 246 optimal weight: 9.9990 chunk 273 optimal weight: 8.9990 chunk 225 optimal weight: 4.9990 chunk 241 optimal weight: 0.9990 chunk 171 optimal weight: 8.9990 chunk 230 optimal weight: 0.1980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3068 r_free = 0.3068 target = 0.048177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.042215 restraints weight = 45721.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.043460 restraints weight = 27616.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.044267 restraints weight = 18554.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.044847 restraints weight = 13514.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.045310 restraints weight = 10451.331| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.4100 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 : 0.540 8.443 34792 Z= 0.273 Chirality : 0.041 0.159 3580 Planarity : 0.004 0.047 4452 Dihedral : 3.870 44.677 3396 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 are not related in a simple way. whole: -0.76 (0.15), residues: 3048 helix: 0.85 (0.14), residues: 1544 sheet: None (None), residues: 0 loop : -2.06 (0.14), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 669 TYR 0.029 0.001 TYR D 621 PHE 0.021 0.001 PHE A 424 TRP 0.018 0.001 TRP D 222 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (25620) covalent geometry : angle 0.54037 / 0.27 (34792) hydrogen bonds : bond 0.02805 / 1.78 ( 916) hydrogen bonds : angle 3.83244 / 2.73 ( 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 58 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.246 Fit side-chains REVERT: A 159 TYR cc_start: 0.6618 (t80) cc_final: 0.5968 (t80) REVERT: A 270 MET cc_start: 0.8603 (mtp) cc_final: 0.8394 (mtp) REVERT: A 466 MET cc_start: 0.7509 (tpp) cc_final: 0.7245 (tpt) REVERT: A 486 LEU cc_start: 0.7888 (tp) cc_final: 0.7658 (tp) REVERT: A 653 ASN cc_start: 0.8762 (m-40) cc_final: 0.8245 (p0) REVERT: A 694 TYR cc_start: 0.8807 (m-80) cc_final: 0.8587 (m-80) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.0790 time to fit residues: 6.3929 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 : 0.213 ------------------------------------------------------------------------------- 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: 5.9990 chunk 184 optimal weight: 10.0000 chunk 213 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 chunk 294 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 153 optimal weight: 0.8980 chunk 214 optimal weight: 9.9990 chunk 200 optimal weight: 10.0000 chunk 174 optimal weight: 7.9990 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3052 r_free = 0.3052 target = 0.047442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.041531 restraints weight = 44124.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.042766 restraints weight = 26655.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.043595 restraints weight = 17826.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.044181 restraints weight = 12886.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.044679 restraints weight = 10016.927| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25620 Z= 0.104 Angle : 0.557 8.382 34792 Z= 0.279 Chirality : 0.041 0.157 3580 Planarity : 0.004 0.047 4452 Dihedral : 3.905 43.014 3396 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % 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 are not related in a simple way. whole: -0.71 (0.15), residues: 3048 helix: 0.91 (0.14), residues: 1544 sheet: None (None), residues: 0 loop : -2.06 (0.14), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 347 TYR 0.026 0.001 TYR B 621 PHE 0.021 0.001 PHE A 424 TRP 0.014 0.001 TRP C 420 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.10 (25620) covalent geometry : angle 0.55742 / 0.28 (34792) hydrogen bonds : bond 0.02827 / 1.80 ( 916) hydrogen bonds : angle 3.82500 / 2.74 ( 2664) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1667.91 seconds wall clock time: 30 minutes 33.65 seconds (1833.65 seconds total)