Starting phenix.real_space_refine on Fri Apr 12 05:24:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5z_35996/04_2024/8j5z_35996_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5z_35996/04_2024/8j5z_35996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5z_35996/04_2024/8j5z_35996.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5z_35996/04_2024/8j5z_35996.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5z_35996/04_2024/8j5z_35996_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5z_35996/04_2024/8j5z_35996_updated.pdb" } resolution = 4.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 164 5.16 5 C 16000 2.51 5 N 4184 2.21 5 O 4508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 24856 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 6194 Classifications: {'peptide': 764} Link IDs: {'PTRANS': 43, 'TRANS': 720} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 6194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 6194 Classifications: {'peptide': 764} Link IDs: {'PTRANS': 43, 'TRANS': 720} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 6194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 6194 Classifications: {'peptide': 764} Link IDs: {'PTRANS': 43, 'TRANS': 720} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 6194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 6194 Classifications: {'peptide': 764} Link IDs: {'PTRANS': 43, 'TRANS': 720} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'BOG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'BOG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'BOG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'BOG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.22, per 1000 atoms: 0.49 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.91 Conformation dependent library (CDL) restraints added in 4.4 seconds 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5656 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 128 helices and 4 sheets defined 47.3% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.28 Creating SS restraints... Processing helix chain 'A' and resid 42 through 55 removed outlier: 3.548A pdb=" N GLU A 46 " --> pdb=" O ALA A 43 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS A 51 " --> pdb=" O ALA A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 74 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 94 through 111 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) Processing helix chain 'A' and resid 129 through 139 Processing helix chain 'A' and resid 142 through 145 No H-bonds generated for 'chain 'A' and resid 142 through 145' Processing helix chain 'A' and resid 148 through 160 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) Processing helix chain 'A' and resid 179 through 190 Processing helix chain 'A' and resid 203 through 213 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) removed outlier: 4.091A pdb=" N HIS A 213 " --> pdb=" O TRP A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 229 removed outlier: 3.532A pdb=" N ILE A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 243 through 246 removed outlier: 4.387A pdb=" N TRP A 246 " --> pdb=" O PRO A 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 243 through 246' Processing helix chain 'A' and resid 261 through 276 Proline residue: A 269 - end of helix Processing helix chain 'A' and resid 284 through 293 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) Processing helix chain 'A' and resid 321 through 334 removed outlier: 3.549A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 364 removed outlier: 3.547A pdb=" N ASN A 364 " --> pdb=" O TYR A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 385 removed outlier: 3.694A pdb=" N GLU A 385 " --> pdb=" O CYS A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 397 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 418 through 431 Processing helix chain 'A' and resid 440 through 452 removed outlier: 4.095A pdb=" N PHE A 449 " --> pdb=" O LYS A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 501 removed outlier: 3.650A pdb=" N GLU A 492 " --> pdb=" O ASP A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 508 No H-bonds generated for 'chain 'A' and resid 505 through 508' Processing helix chain 'A' and resid 516 through 526 removed outlier: 3.551A pdb=" N ALA A 520 " --> pdb=" O TRP A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 549 removed outlier: 3.564A pdb=" N GLU A 547 " --> pdb=" O GLU A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 581 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 587 through 603 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) Processing helix chain 'A' and resid 621 through 633 removed outlier: 3.853A pdb=" N PHE A 625 " --> pdb=" O TYR A 621 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA A 632 " --> pdb=" O GLY A 628 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N THR A 633 " --> pdb=" O GLY A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 652 removed outlier: 3.810A pdb=" N VAL A 647 " --> pdb=" O VAL A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 669 Proline residue: A 668 - end of helix No H-bonds generated for 'chain 'A' and resid 664 through 669' Processing helix chain 'A' and resid 682 through 695 removed outlier: 4.041A pdb=" N ALA A 695 " --> pdb=" O GLY A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 713 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) Processing helix chain 'A' and resid 742 through 757 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 55 removed outlier: 3.547A pdb=" N GLU B 46 " --> pdb=" O ALA B 43 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS B 51 " --> pdb=" O ALA B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 74 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 94 through 111 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) Processing helix chain 'B' and resid 129 through 139 Processing helix chain 'B' and resid 142 through 145 No H-bonds generated for 'chain 'B' and resid 142 through 145' Processing helix chain 'B' and resid 148 through 160 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) Processing helix chain 'B' and resid 179 through 190 Processing helix chain 'B' and resid 203 through 213 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) removed outlier: 4.092A pdb=" N HIS B 213 " --> pdb=" O TRP B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 229 removed outlier: 3.532A pdb=" N ILE B 229 " --> pdb=" O THR B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 237 No H-bonds generated for 'chain 'B' and resid 235 through 237' Processing helix chain 'B' and resid 243 through 246 removed outlier: 4.387A pdb=" N TRP B 246 " --> pdb=" O PRO B 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 243 through 246' Processing helix chain 'B' and resid 261 through 276 Proline residue: B 269 - end of helix Processing helix chain 'B' and resid 284 through 293 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) Processing helix chain 'B' and resid 321 through 334 removed outlier: 3.549A pdb=" N VAL B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 364 removed outlier: 3.546A pdb=" N ASN B 364 " --> pdb=" O TYR B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 385 removed outlier: 3.694A pdb=" N GLU B 385 " --> pdb=" O CYS B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 397 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 418 through 431 Processing helix chain 'B' and resid 440 through 452 removed outlier: 4.095A pdb=" N PHE B 449 " --> pdb=" O LYS B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 501 removed outlier: 3.650A pdb=" N GLU B 492 " --> pdb=" O ASP B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 508 No H-bonds generated for 'chain 'B' and resid 505 through 508' Processing helix chain 'B' and resid 516 through 526 removed outlier: 3.551A pdb=" N ALA B 520 " --> pdb=" O TRP B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 549 removed outlier: 3.565A pdb=" N GLU B 547 " --> pdb=" O GLU B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 581 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 587 through 603 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) Processing helix chain 'B' and resid 621 through 633 removed outlier: 3.853A pdb=" N PHE B 625 " --> pdb=" O TYR B 621 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA B 632 " --> pdb=" O GLY B 628 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N THR B 633 " --> pdb=" O GLY B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 652 removed outlier: 3.810A pdb=" N VAL B 647 " --> pdb=" O VAL B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 669 Proline residue: B 668 - end of helix No H-bonds generated for 'chain 'B' and resid 664 through 669' Processing helix chain 'B' and resid 682 through 695 removed outlier: 4.041A pdb=" N ALA B 695 " --> pdb=" O GLY B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 713 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) Processing helix chain 'B' and resid 742 through 757 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 55 removed outlier: 3.547A pdb=" N GLU C 46 " --> pdb=" O ALA C 43 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS C 51 " --> pdb=" O ALA C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 74 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 94 through 111 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) Processing helix chain 'C' and resid 129 through 139 Processing helix chain 'C' and resid 142 through 145 No H-bonds generated for 'chain 'C' and resid 142 through 145' Processing helix chain 'C' and resid 148 through 160 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) Processing helix chain 'C' and resid 179 through 190 Processing helix chain 'C' and resid 203 through 213 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) removed outlier: 4.092A pdb=" N HIS C 213 " --> pdb=" O TRP C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 229 removed outlier: 3.533A pdb=" N ILE C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 237 No H-bonds generated for 'chain 'C' and resid 235 through 237' Processing helix chain 'C' and resid 243 through 246 removed outlier: 4.387A pdb=" N TRP C 246 " --> pdb=" O PRO C 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 243 through 246' Processing helix chain 'C' and resid 261 through 276 Proline residue: C 269 - end of helix Processing helix chain 'C' and resid 284 through 293 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) Processing helix chain 'C' and resid 321 through 334 removed outlier: 3.548A pdb=" N VAL C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 364 removed outlier: 3.547A pdb=" N ASN C 364 " --> pdb=" O TYR C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 385 removed outlier: 3.694A pdb=" N GLU C 385 " --> pdb=" O CYS C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 397 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 418 through 431 Processing helix chain 'C' and resid 440 through 452 removed outlier: 4.096A pdb=" N PHE C 449 " --> pdb=" O LYS C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 501 removed outlier: 3.651A pdb=" N GLU C 492 " --> pdb=" O ASP C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 508 No H-bonds generated for 'chain 'C' and resid 505 through 508' Processing helix chain 'C' and resid 516 through 526 removed outlier: 3.551A pdb=" N ALA C 520 " --> pdb=" O TRP C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 549 removed outlier: 3.565A pdb=" N GLU C 547 " --> pdb=" O GLU C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 581 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 587 through 603 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) Processing helix chain 'C' and resid 621 through 633 removed outlier: 3.853A pdb=" N PHE C 625 " --> pdb=" O TYR C 621 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA C 632 " --> pdb=" O GLY C 628 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N THR C 633 " --> pdb=" O GLY C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 643 through 652 removed outlier: 3.810A pdb=" N VAL C 647 " --> pdb=" O VAL C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 669 Proline residue: C 668 - end of helix No H-bonds generated for 'chain 'C' and resid 664 through 669' Processing helix chain 'C' and resid 682 through 695 removed outlier: 4.041A pdb=" N ALA C 695 " --> pdb=" O GLY C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 713 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) Processing helix chain 'C' and resid 742 through 757 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 55 removed outlier: 3.547A pdb=" N GLU D 46 " --> pdb=" O ALA D 43 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS D 51 " --> pdb=" O ALA D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 74 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 94 through 111 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) Processing helix chain 'D' and resid 129 through 139 Processing helix chain 'D' and resid 142 through 145 No H-bonds generated for 'chain 'D' and resid 142 through 145' Processing helix chain 'D' and resid 148 through 160 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) Processing helix chain 'D' and resid 179 through 190 Processing helix chain 'D' and resid 203 through 213 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) removed outlier: 4.092A pdb=" N HIS D 213 " --> pdb=" O TRP D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 229 removed outlier: 3.533A pdb=" N ILE D 229 " --> pdb=" O THR D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 237 No H-bonds generated for 'chain 'D' and resid 235 through 237' Processing helix chain 'D' and resid 243 through 246 removed outlier: 4.386A pdb=" N TRP D 246 " --> pdb=" O PRO D 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 243 through 246' Processing helix chain 'D' and resid 261 through 276 Proline residue: D 269 - end of helix Processing helix chain 'D' and resid 284 through 293 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) Processing helix chain 'D' and resid 321 through 334 removed outlier: 3.548A pdb=" N VAL D 332 " --> pdb=" O ASP D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 364 removed outlier: 3.547A pdb=" N ASN D 364 " --> pdb=" O TYR D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 385 removed outlier: 3.694A pdb=" N GLU D 385 " --> pdb=" O CYS D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 397 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 418 through 431 Processing helix chain 'D' and resid 440 through 452 removed outlier: 4.095A pdb=" N PHE D 449 " --> pdb=" O LYS D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 501 removed outlier: 3.650A pdb=" N GLU D 492 " --> pdb=" O ASP D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 508 No H-bonds generated for 'chain 'D' and resid 505 through 508' Processing helix chain 'D' and resid 516 through 526 removed outlier: 3.551A pdb=" N ALA D 520 " --> pdb=" O TRP D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 549 removed outlier: 3.564A pdb=" N GLU D 547 " --> pdb=" O GLU D 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 581 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 587 through 603 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) Processing helix chain 'D' and resid 621 through 633 removed outlier: 3.853A pdb=" N PHE D 625 " --> pdb=" O TYR D 621 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA D 632 " --> pdb=" O GLY D 628 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N THR D 633 " --> pdb=" O GLY D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 643 through 652 removed outlier: 3.809A pdb=" N VAL D 647 " --> pdb=" O VAL D 643 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 669 Proline residue: D 668 - end of helix No H-bonds generated for 'chain 'D' and resid 664 through 669' Processing helix chain 'D' and resid 682 through 695 removed outlier: 4.041A pdb=" N ALA D 695 " --> pdb=" O GLY D 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 703 through 713 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) Processing helix chain 'D' and resid 742 through 757 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= A, 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= B, 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= C, 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= D, 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) 740 hydrogen bonds defined for protein. 2088 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: 6.00 Time building geometry restraints manager: 9.68 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: 100.77 - 107.44: 1225 107.44 - 114.10: 13743 114.10 - 120.77: 11130 120.77 - 127.44: 8257 127.44 - 134.10: 437 Bond angle restraints: 34792 Sorted by residual: angle pdb=" N VAL A 711 " pdb=" CA VAL A 711 " pdb=" C VAL A 711 " ideal model delta sigma weight residual 112.98 110.26 2.72 1.25e+00 6.40e-01 4.72e+00 angle pdb=" N VAL B 711 " pdb=" CA VAL B 711 " pdb=" C VAL B 711 " ideal model delta sigma weight residual 112.98 110.28 2.70 1.25e+00 6.40e-01 4.67e+00 angle pdb=" N VAL C 711 " pdb=" CA VAL C 711 " pdb=" C VAL C 711 " ideal model delta sigma weight residual 112.98 110.30 2.68 1.25e+00 6.40e-01 4.61e+00 angle pdb=" N VAL D 711 " pdb=" CA VAL D 711 " pdb=" C VAL D 711 " ideal model delta sigma weight residual 112.98 110.32 2.66 1.25e+00 6.40e-01 4.54e+00 angle pdb=" CA PRO C 130 " pdb=" C PRO C 130 " pdb=" N PRO C 131 " ideal model delta sigma weight residual 117.93 120.21 -2.28 1.20e+00 6.94e-01 3.60e+00 ... (remaining 34787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.86: 14612 24.86 - 49.72: 343 49.72 - 74.58: 71 74.58 - 99.44: 28 99.44 - 124.30: 14 Dihedral angle restraints: 15068 sinusoidal: 6200 harmonic: 8868 Sorted by residual: dihedral pdb=" C2 BOG C 801 " pdb=" C1 BOG C 801 " pdb=" O5 BOG C 801 " pdb=" C5 BOG C 801 " ideal model delta sinusoidal sigma weight residual -63.97 60.33 -124.30 1 3.00e+01 1.11e-03 1.67e+01 dihedral pdb=" C1 BOG B 801 " pdb=" C2 BOG B 801 " pdb=" C3 BOG B 801 " pdb=" O3 BOG B 801 " ideal model delta sinusoidal sigma weight residual -178.34 -56.75 -121.59 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" O2 BOG B 801 " pdb=" C2 BOG B 801 " pdb=" C3 BOG B 801 " pdb=" O3 BOG B 801 " ideal model delta sinusoidal sigma weight residual 62.09 -176.53 -121.38 1 3.00e+01 1.11e-03 1.62e+01 ... (remaining 15065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2028 0.027 - 0.054: 1010 0.054 - 0.081: 338 0.081 - 0.108: 191 0.108 - 0.135: 13 Chirality restraints: 3580 Sorted by residual: chirality pdb=" CB ILE C 368 " pdb=" CA ILE C 368 " pdb=" CG1 ILE C 368 " pdb=" CG2 ILE C 368 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CB ILE D 368 " pdb=" CA ILE D 368 " pdb=" CG1 ILE D 368 " pdb=" CG2 ILE D 368 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CB ILE B 368 " pdb=" CA ILE B 368 " pdb=" CG1 ILE B 368 " pdb=" CG2 ILE B 368 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 3577 not shown) Planarity restraints: 4452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 129 " 0.033 5.00e-02 4.00e+02 5.00e-02 4.00e+00 pdb=" N PRO A 130 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 130 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 130 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 129 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.98e+00 pdb=" N PRO D 130 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO D 130 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 130 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 129 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO B 130 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 130 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 130 " 0.028 5.00e-02 4.00e+02 ... (remaining 4449 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3871 2.76 - 3.29: 24440 3.29 - 3.83: 40827 3.83 - 4.36: 46369 4.36 - 4.90: 79053 Nonbonded interactions: 194560 Sorted by model distance: nonbonded pdb=" OG1 THR B 177 " pdb=" OD2 ASP B 314 " model vdw 2.224 2.440 nonbonded pdb=" OG1 THR A 177 " pdb=" OD2 ASP A 314 " model vdw 2.224 2.440 nonbonded pdb=" OG1 THR D 177 " pdb=" OD2 ASP D 314 " model vdw 2.224 2.440 nonbonded pdb=" OG1 THR C 177 " pdb=" OD2 ASP C 314 " model vdw 2.224 2.440 nonbonded pdb=" NH1 ARG B 645 " pdb=" OE1 GLN C 641 " model vdw 2.233 2.520 ... (remaining 194555 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 4.370 Check model and map are aligned: 0.390 Set scattering table: 0.240 Process input model: 59.810 Find NCS groups from input model: 1.640 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 25620 Z= 0.128 Angle : 0.468 5.142 34792 Z= 0.244 Chirality : 0.038 0.135 3580 Planarity : 0.004 0.050 4452 Dihedral : 12.557 124.298 9412 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.96 % Allowed : 8.88 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.16), residues: 3048 helix: 0.92 (0.15), residues: 1424 sheet: None (None), residues: 0 loop : -1.94 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 475 HIS 0.002 0.000 HIS C 482 PHE 0.006 0.001 PHE A 183 TYR 0.005 0.001 TYR D 582 ARG 0.001 0.000 ARG D 290 *********************** 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 fitting. rotamer outliers: 26 poor density : 100 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.6133 (OUTLIER) cc_final: 0.5861 (pp) REVERT: A 27 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7333 (tpt90) REVERT: A 159 TYR cc_start: 0.6414 (t80) cc_final: 0.5666 (t80) REVERT: A 193 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8390 (tp) REVERT: A 270 MET cc_start: 0.7978 (mtp) cc_final: 0.7717 (mtp) REVERT: A 349 LYS cc_start: 0.7460 (mmtp) cc_final: 0.7101 (ttmt) REVERT: A 360 TYR cc_start: 0.8360 (OUTLIER) cc_final: 0.7163 (p90) REVERT: A 413 GLN cc_start: 0.7463 (tt0) cc_final: 0.7058 (tt0) REVERT: A 466 MET cc_start: 0.7962 (mmt) cc_final: 0.7599 (tpt) REVERT: A 485 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7471 (mt0) REVERT: A 486 LEU cc_start: 0.8513 (tp) cc_final: 0.8305 (tt) outliers start: 26 outliers final: 7 residues processed: 123 average time/residue: 0.2550 time to fit residues: 38.9733 Evaluate side-chains 61 residues out of total 658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 49 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 0.6980 chunk 230 optimal weight: 0.0770 chunk 127 optimal weight: 4.9990 chunk 78 optimal weight: 0.0370 chunk 155 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 238 optimal weight: 10.0000 chunk 92 optimal weight: 0.0270 chunk 144 optimal weight: 5.9990 chunk 177 optimal weight: 7.9990 chunk 276 optimal weight: 20.0000 overall best weight: 0.7676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 91 GLN ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 25620 Z= 0.163 Angle : 0.557 7.194 34792 Z= 0.282 Chirality : 0.042 0.206 3580 Planarity : 0.005 0.057 4452 Dihedral : 8.954 79.002 3492 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.15), residues: 3048 helix: 0.60 (0.14), residues: 1460 sheet: None (None), residues: 0 loop : -2.07 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 30 HIS 0.008 0.001 HIS A 299 PHE 0.023 0.002 PHE C 183 TYR 0.027 0.001 TYR B 360 ARG 0.007 0.000 ARG C 366 *********************** 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 65 residues out of total 658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 TYR cc_start: 0.6517 (t80) cc_final: 0.5760 (t80) REVERT: A 270 MET cc_start: 0.8116 (mtp) cc_final: 0.7870 (mtp) REVERT: A 466 MET cc_start: 0.7648 (mmt) cc_final: 0.7353 (tpt) REVERT: A 499 LEU cc_start: 0.8012 (pp) cc_final: 0.7732 (pp) REVERT: A 694 TYR cc_start: 0.8842 (m-80) cc_final: 0.8614 (m-80) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.2027 time to fit residues: 17.8341 Evaluate side-chains 44 residues out of total 658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 0.0020 chunk 85 optimal weight: 0.0030 chunk 229 optimal weight: 0.7980 chunk 187 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 276 optimal weight: 10.0000 chunk 298 optimal weight: 0.7980 chunk 246 optimal weight: 10.0000 chunk 274 optimal weight: 20.0000 chunk 94 optimal weight: 8.9990 chunk 221 optimal weight: 10.0000 overall best weight: 2.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2872 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= 0.153 Angle : 0.523 8.273 34792 Z= 0.259 Chirality : 0.040 0.174 3580 Planarity : 0.004 0.045 4452 Dihedral : 6.679 58.465 3492 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.15), residues: 3048 helix: 0.65 (0.14), residues: 1436 sheet: None (None), residues: 0 loop : -2.04 (0.14), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 30 HIS 0.005 0.001 HIS C 299 PHE 0.021 0.001 PHE C 183 TYR 0.015 0.001 TYR C 360 ARG 0.003 0.000 ARG B 366 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: A 159 TYR cc_start: 0.6533 (t80) cc_final: 0.5765 (t80) REVERT: A 270 MET cc_start: 0.8115 (mtp) cc_final: 0.7887 (mtp) REVERT: A 694 TYR cc_start: 0.8831 (m-80) cc_final: 0.8504 (m-80) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1757 time to fit residues: 13.8212 Evaluate side-chains 41 residues out of total 658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 273 optimal weight: 0.0070 chunk 207 optimal weight: 0.0970 chunk 143 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 131 optimal weight: 0.1980 chunk 185 optimal weight: 10.0000 chunk 277 optimal weight: 7.9990 chunk 293 optimal weight: 0.7980 chunk 145 optimal weight: 0.8980 chunk 263 optimal weight: 9.9990 chunk 79 optimal weight: 0.0470 overall best weight: 0.2294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 25620 Z= 0.122 Angle : 0.498 5.229 34792 Z= 0.250 Chirality : 0.039 0.157 3580 Planarity : 0.004 0.046 4452 Dihedral : 4.791 51.543 3492 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.15), residues: 3048 helix: 0.56 (0.14), residues: 1444 sheet: None (None), residues: 0 loop : -2.08 (0.14), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 420 HIS 0.003 0.000 HIS C 308 PHE 0.015 0.001 PHE D 183 TYR 0.009 0.001 TYR C 360 ARG 0.002 0.000 ARG D 678 *********************** 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 53 residues out of total 658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.756 Fit side-chains revert: symmetry clash REVERT: A 159 TYR cc_start: 0.6479 (t80) cc_final: 0.5700 (t80) REVERT: A 546 MET cc_start: 0.8255 (mmt) cc_final: 0.8013 (mmt) REVERT: A 694 TYR cc_start: 0.8777 (m-80) cc_final: 0.8457 (m-80) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1650 time to fit residues: 12.7043 Evaluate side-chains 42 residues out of total 658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 244 optimal weight: 1.9990 chunk 166 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 218 optimal weight: 20.0000 chunk 121 optimal weight: 0.0570 chunk 250 optimal weight: 10.0000 chunk 203 optimal weight: 0.0670 chunk 0 optimal weight: 10.0000 chunk 150 optimal weight: 8.9990 chunk 263 optimal weight: 8.9990 chunk 74 optimal weight: 9.9990 overall best weight: 3.4242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 HIS ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3274 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= 0.162 Angle : 0.497 5.215 34792 Z= 0.254 Chirality : 0.040 0.167 3580 Planarity : 0.004 0.045 4452 Dihedral : 4.423 47.750 3492 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % 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 : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.15), residues: 3048 helix: 0.76 (0.15), residues: 1440 sheet: None (None), residues: 0 loop : -1.99 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 420 HIS 0.003 0.001 HIS C 308 PHE 0.023 0.002 PHE C 619 TYR 0.013 0.001 TYR A 360 ARG 0.002 0.000 ARG D 599 *********************** 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 fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.741 Fit side-chains REVERT: A 159 TYR cc_start: 0.6478 (t80) cc_final: 0.5747 (t80) REVERT: A 241 MET cc_start: 0.7393 (tpt) cc_final: 0.6543 (mtm) REVERT: A 694 TYR cc_start: 0.8812 (m-80) cc_final: 0.8544 (m-80) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1455 time to fit residues: 11.4942 Evaluate side-chains 41 residues out of total 658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 98 optimal weight: 0.0970 chunk 264 optimal weight: 0.0980 chunk 58 optimal weight: 8.9990 chunk 172 optimal weight: 0.3980 chunk 72 optimal weight: 10.0000 chunk 294 optimal weight: 20.0000 chunk 244 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 97 optimal weight: 9.9990 chunk 154 optimal weight: 20.0000 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN A 395 HIS ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 25620 Z= 0.130 Angle : 0.521 6.184 34792 Z= 0.259 Chirality : 0.039 0.139 3580 Planarity : 0.004 0.046 4452 Dihedral : 4.328 49.323 3492 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.15), residues: 3048 helix: 0.62 (0.14), residues: 1444 sheet: None (None), residues: 0 loop : -1.97 (0.15), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 2 HIS 0.002 0.000 HIS D 308 PHE 0.016 0.001 PHE C 619 TYR 0.015 0.001 TYR A 360 ARG 0.001 0.000 ARG D 366 *********************** 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 55 residues out of total 658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.695 Fit side-chains REVERT: A 159 TYR cc_start: 0.6424 (t80) cc_final: 0.5680 (t80) REVERT: A 241 MET cc_start: 0.7475 (tpt) cc_final: 0.6466 (mtm) REVERT: A 270 MET cc_start: 0.9153 (mpp) cc_final: 0.8196 (mpp) REVERT: A 694 TYR cc_start: 0.8751 (m-80) cc_final: 0.8519 (m-80) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1464 time to fit residues: 12.1823 Evaluate side-chains 40 residues out of total 658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 283 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 167 optimal weight: 0.9980 chunk 214 optimal weight: 9.9990 chunk 166 optimal weight: 6.9990 chunk 247 optimal weight: 0.0060 chunk 164 optimal weight: 1.9990 chunk 293 optimal weight: 7.9990 chunk 183 optimal weight: 0.0020 chunk 178 optimal weight: 0.0040 chunk 135 optimal weight: 6.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 25620 Z= 0.126 Angle : 0.520 12.830 34792 Z= 0.251 Chirality : 0.040 0.152 3580 Planarity : 0.004 0.045 4452 Dihedral : 4.249 45.982 3492 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.15), residues: 3048 helix: 0.68 (0.14), residues: 1444 sheet: None (None), residues: 0 loop : -1.96 (0.14), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 2 HIS 0.006 0.001 HIS C 395 PHE 0.013 0.001 PHE A 179 TYR 0.017 0.001 TYR A 360 ARG 0.001 0.000 ARG B 678 *********************** 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 56 residues out of total 658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.711 Fit side-chains REVERT: A 159 TYR cc_start: 0.6436 (t80) cc_final: 0.5679 (t80) REVERT: A 241 MET cc_start: 0.7532 (tpt) cc_final: 0.6354 (mtm) REVERT: A 270 MET cc_start: 0.9106 (mpp) cc_final: 0.8212 (mpp) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1475 time to fit residues: 12.1990 Evaluate side-chains 40 residues out of total 658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 181 optimal weight: 2.9990 chunk 117 optimal weight: 0.3980 chunk 174 optimal weight: 10.0000 chunk 88 optimal weight: 0.0060 chunk 57 optimal weight: 7.9990 chunk 56 optimal weight: 0.0050 chunk 186 optimal weight: 7.9990 chunk 199 optimal weight: 10.0000 chunk 144 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 230 optimal weight: 6.9990 overall best weight: 0.8814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 HIS A 413 GLN ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.3635 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= 0.131 Angle : 0.534 10.485 34792 Z= 0.260 Chirality : 0.040 0.149 3580 Planarity : 0.004 0.047 4452 Dihedral : 4.246 44.764 3492 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.15), residues: 3048 helix: 0.56 (0.14), residues: 1464 sheet: None (None), residues: 0 loop : -2.00 (0.14), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 545 HIS 0.005 0.001 HIS A 395 PHE 0.018 0.001 PHE B 132 TYR 0.011 0.001 TYR D 694 ARG 0.001 0.000 ARG D 678 *********************** 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 51 residues out of total 658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.752 Fit side-chains REVERT: A 159 TYR cc_start: 0.6422 (t80) cc_final: 0.5684 (t80) REVERT: A 270 MET cc_start: 0.9104 (mpp) cc_final: 0.8416 (mpp) REVERT: A 466 MET cc_start: 0.6954 (mmm) cc_final: 0.6537 (tmm) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1394 time to fit residues: 10.9739 Evaluate side-chains 37 residues out of total 658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 266 optimal weight: 7.9990 chunk 280 optimal weight: 4.9990 chunk 256 optimal weight: 5.9990 chunk 273 optimal weight: 7.9990 chunk 164 optimal weight: 0.5980 chunk 118 optimal weight: 9.9990 chunk 214 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 246 optimal weight: 10.0000 chunk 258 optimal weight: 0.3980 chunk 272 optimal weight: 7.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 25620 Z= 0.160 Angle : 0.548 8.795 34792 Z= 0.272 Chirality : 0.040 0.154 3580 Planarity : 0.004 0.046 4452 Dihedral : 4.284 44.869 3492 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.15), residues: 3048 helix: 0.66 (0.14), residues: 1472 sheet: None (None), residues: 0 loop : -1.98 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 209 HIS 0.003 0.001 HIS C 357 PHE 0.022 0.001 PHE B 179 TYR 0.023 0.001 TYR D 694 ARG 0.001 0.000 ARG A 599 *********************** 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 49 residues out of total 658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.706 Fit side-chains REVERT: A 159 TYR cc_start: 0.6345 (t80) cc_final: 0.5679 (t80) REVERT: A 270 MET cc_start: 0.9035 (mpp) cc_final: 0.8350 (mpp) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1449 time to fit residues: 10.7850 Evaluate side-chains 38 residues out of total 658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 179 optimal weight: 0.9980 chunk 288 optimal weight: 0.0060 chunk 176 optimal weight: 0.0970 chunk 136 optimal weight: 0.7980 chunk 200 optimal weight: 7.9990 chunk 302 optimal weight: 0.6980 chunk 278 optimal weight: 4.9990 chunk 241 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 147 optimal weight: 20.0000 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3839 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= 0.130 Angle : 0.550 9.310 34792 Z= 0.267 Chirality : 0.040 0.143 3580 Planarity : 0.004 0.047 4452 Dihedral : 4.224 44.316 3492 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.15), residues: 3048 helix: 0.59 (0.14), residues: 1472 sheet: None (None), residues: 0 loop : -1.98 (0.14), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 420 HIS 0.002 0.000 HIS C 359 PHE 0.025 0.001 PHE C 424 TYR 0.022 0.001 TYR C 694 ARG 0.002 0.000 ARG C 156 ********************** 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 49 residues out of total 658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.651 Fit side-chains REVERT: A 159 TYR cc_start: 0.6367 (t80) cc_final: 0.5663 (t80) REVERT: A 270 MET cc_start: 0.9034 (mpp) cc_final: 0.8353 (mpp) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1444 time to fit residues: 10.7797 Evaluate side-chains 39 residues out of total 658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 191 optimal weight: 2.9990 chunk 256 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 222 optimal weight: 0.0070 chunk 35 optimal weight: 10.0000 chunk 67 optimal weight: 0.1980 chunk 241 optimal weight: 7.9990 chunk 101 optimal weight: 0.1980 chunk 248 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 overall best weight: 1.2802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 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 = 0.3106 r_free = 0.3106 target = 0.049322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.043166 restraints weight = 45654.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.044414 restraints weight = 28581.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.045257 restraints weight = 19618.851| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 25620 Z= 0.134 Angle : 0.549 8.410 34792 Z= 0.269 Chirality : 0.040 0.146 3580 Planarity : 0.004 0.046 4452 Dihedral : 4.207 43.602 3492 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.15), residues: 3048 helix: 0.65 (0.14), residues: 1476 sheet: None (None), residues: 0 loop : -2.00 (0.14), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 420 HIS 0.002 0.001 HIS C 255 PHE 0.020 0.001 PHE D 424 TYR 0.021 0.001 TYR D 694 ARG 0.001 0.000 ARG B 366 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2824.74 seconds wall clock time: 54 minutes 12.01 seconds (3252.01 seconds total)