Starting phenix.real_space_refine on Tue Nov 19 01:14:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3w_17397/11_2024/8p3w_17397_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3w_17397/11_2024/8p3w_17397.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3w_17397/11_2024/8p3w_17397.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3w_17397/11_2024/8p3w_17397.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3w_17397/11_2024/8p3w_17397_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3w_17397/11_2024/8p3w_17397_neut.cif" } resolution = 3.53 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= 0.001 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 104 5.16 5 C 11462 2.51 5 N 2778 2.21 5 O 3135 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 17485 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2894 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 393, 2876 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 379} Chain breaks: 3 Unresolved non-hydrogen bonds: 232 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 201 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 150 Conformer: "B" Number of residues, atoms: 393, 2876 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 379} Chain breaks: 3 Unresolved non-hydrogen bonds: 232 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 201 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 150 bond proxies already assigned to first conformer: 2922 Chain: "B" Number of atoms: 2933 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 385, 2886 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 372} Chain breaks: 4 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 5, 'GLU:plan': 9, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 100 Conformer: "B" Number of residues, atoms: 385, 2886 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 372} Chain breaks: 4 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 5, 'GLU:plan': 9, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 100 bond proxies already assigned to first conformer: 2900 Chain: "C" Number of atoms: 2868 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 385, 2850 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 372} Chain breaks: 4 Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 113 Conformer: "B" Number of residues, atoms: 385, 2850 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 372} Chain breaks: 4 Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 113 bond proxies already assigned to first conformer: 2895 Chain: "D" Number of atoms: 2899 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 384, 2852 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 371} Chain breaks: 4 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 215 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 120 Conformer: "B" Number of residues, atoms: 384, 2852 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 371} Chain breaks: 4 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 215 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 120 bond proxies already assigned to first conformer: 2864 Chain: "E" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1367 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Chain: "F" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1367 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Chain: "G" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1367 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Chain: "H" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1367 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'OLC': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 82 Unusual residues: {'OLC': 1, 'PLM': 1, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'OLC': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 82 Unusual residues: {'OLC': 1, 'PLM': 1, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 19 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 19 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 18 residue: pdb=" N AGLY A 584 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 584 " occ=0.50 residue: pdb=" N ACYS A 585 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 585 " occ=0.50 residue: pdb=" N AASP A 586 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP A 586 " occ=0.50 residue: pdb=" N APHE B 570 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 570 " occ=0.50 residue: pdb=" N AGLN B 582 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B 582 " occ=0.50 residue: pdb=" N AGLN B 583 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B 583 " occ=0.50 residue: pdb=" N AGLY B 584 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY B 584 " occ=0.50 residue: pdb=" N ACYS B 585 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 585 " occ=0.50 residue: pdb=" N AASP B 586 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP B 586 " occ=0.50 residue: pdb=" N AGLY C 584 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY C 584 " occ=0.50 residue: pdb=" N ACYS C 585 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS C 585 " occ=0.50 residue: pdb=" N AASP C 586 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP C 586 " occ=0.50 ... (remaining 6 not shown) Time building chain proxies: 15.03, per 1000 atoms: 0.86 Number of scatterers: 17485 At special positions: 0 Unit cell: (111.3, 107.325, 136.475, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 104 16.00 P 6 15.00 O 3135 8.00 N 2778 7.00 C 11462 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.01 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.05 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.02 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.05 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.03 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: 4.61 Conformation dependent library (CDL) restraints added in 3.9 seconds 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4138 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 28 sheets defined 62.3% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'A' and resid 407 through 411 removed outlier: 3.584A pdb=" N GLN A 410 " --> pdb=" O ASN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 415 removed outlier: 4.185A pdb=" N ASP A 415 " --> pdb=" O GLU A 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 412 through 415' Processing helix chain 'A' and resid 419 through 433 Processing helix chain 'A' and resid 458 through 465 Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 518 through 542 Processing helix chain 'A' and resid 568 through 581 Processing helix chain 'A' and resid 591 through 626 removed outlier: 4.864A pdb=" N GLU A 623 " --> pdb=" O PHE A 619 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG A 624 " --> pdb=" O LEU A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 638 removed outlier: 3.680A pdb=" N LEU A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN A 638 " --> pdb=" O ASP A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 657 Processing helix chain 'A' and resid 660 through 673 Processing helix chain 'A' and resid 681 through 691 Processing helix chain 'A' and resid 702 through 710 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 753 through 764 Processing helix chain 'A' and resid 784 through 787 Processing helix chain 'A' and resid 788 through 814 removed outlier: 3.510A pdb=" N PHE A 792 " --> pdb=" O VAL A 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 411 removed outlier: 3.604A pdb=" N GLN B 410 " --> pdb=" O ASN B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 415 No H-bonds generated for 'chain 'B' and resid 413 through 415' Processing helix chain 'B' and resid 419 through 433 Processing helix chain 'B' and resid 457 through 465 Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 511 through 515 Processing helix chain 'B' and resid 518 through 542 Processing helix chain 'B' and resid 568 through 581 Processing helix chain 'B' and resid 591 through 623 Processing helix chain 'B' and resid 631 through 638 Processing helix chain 'B' and resid 649 through 657 Processing helix chain 'B' and resid 660 through 673 removed outlier: 3.618A pdb=" N SER B 672 " --> pdb=" O THR B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 692 Processing helix chain 'B' and resid 702 through 711 Processing helix chain 'B' and resid 738 through 752 Processing helix chain 'B' and resid 753 through 763 Processing helix chain 'B' and resid 784 through 787 Processing helix chain 'B' and resid 788 through 815 removed outlier: 3.585A pdb=" N PHE B 792 " --> pdb=" O VAL B 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 411 removed outlier: 3.586A pdb=" N GLN C 410 " --> pdb=" O ASN C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 415 removed outlier: 4.195A pdb=" N ASP C 415 " --> pdb=" O GLU C 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 412 through 415' Processing helix chain 'C' and resid 419 through 433 Processing helix chain 'C' and resid 458 through 465 Processing helix chain 'C' and resid 478 through 483 Processing helix chain 'C' and resid 511 through 515 Processing helix chain 'C' and resid 518 through 542 Processing helix chain 'C' and resid 568 through 581 Processing helix chain 'C' and resid 591 through 622 Processing helix chain 'C' and resid 631 through 638 removed outlier: 3.618A pdb=" N LEU C 635 " --> pdb=" O SER C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 657 Processing helix chain 'C' and resid 660 through 672 Processing helix chain 'C' and resid 681 through 691 Processing helix chain 'C' and resid 702 through 711 Processing helix chain 'C' and resid 738 through 752 Processing helix chain 'C' and resid 753 through 764 Processing helix chain 'C' and resid 784 through 787 Processing helix chain 'C' and resid 788 through 814 removed outlier: 3.563A pdb=" N PHE C 792 " --> pdb=" O VAL C 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 415 removed outlier: 4.247A pdb=" N ASP D 415 " --> pdb=" O GLU D 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 412 through 415' Processing helix chain 'D' and resid 419 through 433 Processing helix chain 'D' and resid 457 through 466 Processing helix chain 'D' and resid 478 through 483 Processing helix chain 'D' and resid 511 through 515 Processing helix chain 'D' and resid 518 through 542 Processing helix chain 'D' and resid 568 through 581 Processing helix chain 'D' and resid 591 through 622 Processing helix chain 'D' and resid 631 through 638 Processing helix chain 'D' and resid 649 through 657 Processing helix chain 'D' and resid 660 through 673 removed outlier: 3.599A pdb=" N SER D 672 " --> pdb=" O THR D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 681 through 692 Processing helix chain 'D' and resid 702 through 711 Processing helix chain 'D' and resid 738 through 752 Processing helix chain 'D' and resid 753 through 764 Processing helix chain 'D' and resid 784 through 787 Processing helix chain 'D' and resid 788 through 815 removed outlier: 3.589A pdb=" N PHE D 792 " --> pdb=" O VAL D 788 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 30 Processing helix chain 'E' and resid 93 through 105 Processing helix chain 'E' and resid 105 through 128 removed outlier: 4.254A pdb=" N GLU E 126 " --> pdb=" O VAL E 122 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE E 127 " --> pdb=" O ALA E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 162 removed outlier: 3.924A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 209 removed outlier: 3.583A pdb=" N TYR E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 30 Processing helix chain 'F' and resid 93 through 105 Processing helix chain 'F' and resid 105 through 126 removed outlier: 3.811A pdb=" N GLU F 126 " --> pdb=" O VAL F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 162 removed outlier: 3.757A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 209 removed outlier: 3.550A pdb=" N TYR F 180 " --> pdb=" O GLY F 176 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG F 208 " --> pdb=" O HIS F 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 30 Processing helix chain 'G' and resid 93 through 105 Processing helix chain 'G' and resid 105 through 128 removed outlier: 4.193A pdb=" N GLU G 126 " --> pdb=" O VAL G 122 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 162 removed outlier: 3.872A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 209 removed outlier: 3.592A pdb=" N TYR G 180 " --> pdb=" O GLY G 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 30 Processing helix chain 'H' and resid 93 through 105 Processing helix chain 'H' and resid 105 through 126 removed outlier: 3.759A pdb=" N GLU H 126 " --> pdb=" O VAL H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 162 removed outlier: 3.800A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY H 162 " --> pdb=" O SER H 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 209 removed outlier: 3.545A pdb=" N TYR H 180 " --> pdb=" O GLY H 176 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG H 208 " --> pdb=" O HIS H 204 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 440 removed outlier: 3.523A pdb=" N VAL A 470 " --> pdb=" O ILE A 392 " (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 447 through 449 removed outlier: 3.702A pdb=" N ALA A 448 " --> pdb=" O ASN A 457 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 485 through 487 Processing sheet with id=AA5, first strand: chain 'A' and resid 492 through 494 removed outlier: 4.090A pdb=" N MET A 492 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 642 through 644 removed outlier: 6.596A pdb=" N ALA A 642 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N LEU A 699 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLY A 644 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N GLU A 701 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N TYR A 696 " --> pdb=" O LYS A 501 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N LYS A 501 " --> pdb=" O TYR A 696 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 436 through 440 removed outlier: 6.701A pdb=" N TYR B 391 " --> pdb=" O ARG B 437 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLU B 439 " --> pdb=" O TYR B 391 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N VAL B 393 " --> pdb=" O GLU B 439 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL B 470 " --> pdb=" O ILE B 392 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 403 through 404 Processing sheet with id=AA9, first strand: chain 'B' and resid 485 through 487 Processing sheet with id=AB1, first strand: chain 'B' and resid 492 through 494 removed outlier: 3.923A pdb=" N MET B 492 " --> pdb=" O TYR B 728 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 642 through 644 removed outlier: 6.494A pdb=" N ALA B 642 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N LEU B 699 " --> pdb=" O ALA B 642 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY B 644 " --> pdb=" O LEU B 699 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N GLU B 701 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N TYR B 696 " --> pdb=" O LYS B 501 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LYS B 501 " --> pdb=" O TYR B 696 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE B 498 " --> pdb=" O VAL B 719 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 435 through 440 Processing sheet with id=AB4, first strand: chain 'C' and resid 403 through 404 Processing sheet with id=AB5, first strand: chain 'C' and resid 447 through 449 removed outlier: 3.806A pdb=" N ALA C 448 " --> pdb=" O ASN C 457 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 485 through 487 Processing sheet with id=AB7, first strand: chain 'C' and resid 492 through 494 removed outlier: 3.917A pdb=" N MET C 492 " --> pdb=" O TYR C 728 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 642 through 644 removed outlier: 6.575A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 8.883A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 436 through 440 removed outlier: 6.335A pdb=" N TYR D 391 " --> pdb=" O ARG D 437 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLU D 439 " --> pdb=" O TYR D 391 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N VAL D 393 " --> pdb=" O GLU D 439 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL D 470 " --> pdb=" O ILE D 392 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 403 through 404 Processing sheet with id=AC2, first strand: chain 'D' and resid 485 through 487 Processing sheet with id=AC3, first strand: chain 'D' and resid 492 through 494 removed outlier: 3.887A pdb=" N MET D 492 " --> pdb=" O TYR D 728 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 642 through 644 removed outlier: 6.574A pdb=" N ALA D 642 " --> pdb=" O ALA D 697 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU D 699 " --> pdb=" O ALA D 642 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLY D 644 " --> pdb=" O LEU D 699 " (cutoff:3.500A) removed outlier: 8.908A pdb=" N GLU D 701 " --> pdb=" O GLY D 644 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N TYR D 696 " --> pdb=" O LYS D 501 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LYS D 501 " --> pdb=" O TYR D 696 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE D 498 " --> pdb=" O VAL D 719 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 34 through 35 Processing sheet with id=AC6, first strand: chain 'E' and resid 37 through 38 Processing sheet with id=AC7, first strand: chain 'F' and resid 77 through 79 Processing sheet with id=AC8, first strand: chain 'G' and resid 34 through 35 Processing sheet with id=AC9, first strand: chain 'G' and resid 37 through 38 Processing sheet with id=AD1, first strand: chain 'H' and resid 77 through 79 1135 hydrogen bonds defined for protein. 3306 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: 5.69 Time building geometry restraints manager: 5.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 2642 1.27 - 1.42: 4780 1.42 - 1.56: 10224 1.56 - 1.70: 19 1.70 - 1.85: 164 Bond restraints: 17829 Sorted by residual: bond pdb=" C BGLY A 584 " pdb=" O BGLY A 584 " ideal model delta sigma weight residual 1.230 1.403 -0.173 1.58e-02 4.01e+03 1.19e+02 bond pdb=" C BGLY C 584 " pdb=" O BGLY C 584 " ideal model delta sigma weight residual 1.232 1.396 -0.165 1.81e-02 3.05e+03 8.27e+01 bond pdb=" C ACYS B 585 " pdb=" O ACYS B 585 " ideal model delta sigma weight residual 1.234 1.330 -0.096 1.20e-02 6.94e+03 6.36e+01 bond pdb=" C AGLN B 583 " pdb=" O AGLN B 583 " ideal model delta sigma weight residual 1.237 1.129 0.108 1.36e-02 5.41e+03 6.26e+01 bond pdb=" C ACYS A 585 " pdb=" O ACYS A 585 " ideal model delta sigma weight residual 1.234 1.312 -0.077 1.20e-02 6.94e+03 4.17e+01 ... (remaining 17824 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.12: 24049 7.12 - 14.25: 52 14.25 - 21.37: 7 21.37 - 28.50: 2 28.50 - 35.62: 1 Bond angle restraints: 24111 Sorted by residual: angle pdb=" N ALA D 661 " pdb=" CA ALA D 661 " pdb=" CB ALA D 661 " ideal model delta sigma weight residual 110.49 74.87 35.62 1.69e+00 3.50e-01 4.44e+02 angle pdb=" N ACYS B 585 " pdb=" CA ACYS B 585 " pdb=" CB ACYS B 585 " ideal model delta sigma weight residual 111.21 87.24 23.97 1.67e+00 3.59e-01 2.06e+02 angle pdb=" N BCYS D 585 " pdb=" CA BCYS D 585 " pdb=" CB BCYS D 585 " ideal model delta sigma weight residual 110.49 134.47 -23.98 1.69e+00 3.50e-01 2.01e+02 angle pdb=" N ACYS D 585 " pdb=" CA ACYS D 585 " pdb=" CB ACYS D 585 " ideal model delta sigma weight residual 110.97 90.21 20.76 1.56e+00 4.11e-01 1.77e+02 angle pdb=" N BCYS C 585 " pdb=" CA BCYS C 585 " pdb=" CB BCYS C 585 " ideal model delta sigma weight residual 110.97 129.20 -18.23 1.56e+00 4.11e-01 1.36e+02 ... (remaining 24106 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.00: 9540 23.00 - 46.01: 644 46.01 - 69.01: 134 69.01 - 92.01: 24 92.01 - 115.02: 1 Dihedral angle restraints: 10343 sinusoidal: 3858 harmonic: 6485 Sorted by residual: dihedral pdb=" N BCYS C 585 " pdb=" C BCYS C 585 " pdb=" CA BCYS C 585 " pdb=" CB BCYS C 585 " ideal model delta harmonic sigma weight residual 122.80 171.94 -49.14 0 2.50e+00 1.60e-01 3.86e+02 dihedral pdb=" N BCYS A 585 " pdb=" C BCYS A 585 " pdb=" CA BCYS A 585 " pdb=" CB BCYS A 585 " ideal model delta harmonic sigma weight residual 122.80 171.20 -48.40 0 2.50e+00 1.60e-01 3.75e+02 dihedral pdb=" C BCYS C 585 " pdb=" N BCYS C 585 " pdb=" CA BCYS C 585 " pdb=" CB BCYS C 585 " ideal model delta harmonic sigma weight residual -122.60 -170.09 47.49 0 2.50e+00 1.60e-01 3.61e+02 ... (remaining 10340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.425: 2730 0.425 - 0.851: 4 0.851 - 1.276: 0 1.276 - 1.702: 2 1.702 - 2.127: 2 Chirality restraints: 2738 Sorted by residual: chirality pdb=" CA BCYS C 585 " pdb=" N BCYS C 585 " pdb=" C BCYS C 585 " pdb=" CB BCYS C 585 " both_signs ideal model delta sigma weight residual False 2.51 0.38 2.13 2.00e-01 2.50e+01 1.13e+02 chirality pdb=" CA BCYS A 585 " pdb=" N BCYS A 585 " pdb=" C BCYS A 585 " pdb=" CB BCYS A 585 " both_signs ideal model delta sigma weight residual False 2.51 0.43 2.08 2.00e-01 2.50e+01 1.08e+02 chirality pdb=" CA BCYS D 585 " pdb=" N BCYS D 585 " pdb=" C BCYS D 585 " pdb=" CB BCYS D 585 " both_signs ideal model delta sigma weight residual False 2.51 1.09 1.42 2.00e-01 2.50e+01 5.06e+01 ... (remaining 2735 not shown) Planarity restraints: 2952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV F1301 " -0.072 2.00e-02 2.50e+03 1.43e-01 2.05e+02 pdb=" C29 POV F1301 " 0.188 2.00e-02 2.50e+03 pdb="C210 POV F1301 " -0.190 2.00e-02 2.50e+03 pdb="C211 POV F1301 " 0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV H1301 " 0.063 2.00e-02 2.50e+03 1.22e-01 1.49e+02 pdb=" C29 POV H1301 " -0.160 2.00e-02 2.50e+03 pdb="C210 POV H1301 " 0.161 2.00e-02 2.50e+03 pdb="C211 POV H1301 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLC D1002 " -0.152 2.00e-02 2.50e+03 1.14e-01 1.31e+02 pdb=" C11 OLC D1002 " 0.058 2.00e-02 2.50e+03 pdb=" C8 OLC D1002 " -0.057 2.00e-02 2.50e+03 pdb=" C9 OLC D1002 " 0.151 2.00e-02 2.50e+03 ... (remaining 2949 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 83 2.57 - 3.15: 14893 3.15 - 3.74: 26900 3.74 - 4.32: 38729 4.32 - 4.90: 63449 Nonbonded interactions: 144054 Sorted by model distance: nonbonded pdb=" N SER A 725 " pdb=" O LYS D 659 " model vdw 1.988 3.120 nonbonded pdb=" O GLY A 720 " pdb=" NZ LYS D 665 " model vdw 2.051 3.120 nonbonded pdb=" CB ALA D 661 " pdb=" N VAL D 662 " model vdw 2.218 2.832 nonbonded pdb=" N GLU G 55 " pdb=" OE1 GLU G 55 " model vdw 2.304 3.120 nonbonded pdb=" N GLU E 55 " pdb=" OE1 GLU E 55 " model vdw 2.304 3.120 ... (remaining 144049 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 389 through 391 and (name N or name CA or name C or name \ O or name CB )) or resid 392 through 414 or (resid 415 through 416 and (name N o \ r name CA or name C or name O or name CB )) or resid 417 through 429 or (resid 4 \ 30 and (name N or name CA or name C or name O or name CB )) or resid 431 through \ 444 or (resid 445 and (name N or name CA or name C or name O or name CB )) or r \ esid 446 through 502 or resid 508 through 546 or resid 567 through 569 or resid \ 571 through 581 or resid 587 through 622 or resid 630 through 664 or (resid 665 \ and (name N or name CA or name C or name O or name CB )) or resid 666 through 81 \ 5 or resid 1001 through 1002)) selection = (chain 'B' and ((resid 389 through 391 and (name N or name CA or name C or name \ O or name CB )) or resid 392 through 398 or (resid 399 and (name N or name CA or \ name C or name O or name CB )) or resid 400 through 403 or (resid 404 and (name \ N or name CA or name C or name O or name CB )) or resid 405 through 415 or (res \ id 416 and (name N or name CA or name C or name O or name CB )) or resid 417 thr \ ough 429 or (resid 430 and (name N or name CA or name C or name O or name CB )) \ or resid 431 through 444 or (resid 445 and (name N or name CA or name C or name \ O or name CB )) or resid 446 through 461 or (resid 462 and (name N or name CA or \ name C or name O or name CB )) or resid 463 through 500 or (resid 501 through 5 \ 02 and (name N or name CA or name C or name O or name CB )) or resid 508 through \ 545 or (resid 566 and (name N or name CA or name C or name O or name CB )) or r \ esid 567 through 569 or resid 571 through 581 or resid 587 through 618 or (resid \ 619 and (name N or name CA or name C or name O or name CB )) or resid 620 throu \ gh 622 or resid 630 through 632 or (resid 633 through 634 and (name N or name CA \ or name C or name O or name CB )) or resid 635 through 658 or (resid 659 and (n \ ame N or name CA or name C or name O or name CB )) or resid 660 through 664 or ( \ resid 665 and (name N or name CA or name C or name O or name CB )) or resid 666 \ through 683 or (resid 684 and (name N or name CA or name C or name O or name CB \ )) or resid 685 through 687 or (resid 688 and (name N or name CA or name C or na \ me O or name CB )) or resid 689 through 690 or (resid 691 through 693 and (name \ N or name CA or name C or name O or name CB )) or resid 694 through 705 or (resi \ d 706 and (name N or name CA or name C or name O or name CB )) or resid 707 thro \ ugh 813 or (resid 814 through 815 and (name N or name CA or name C or name O or \ name CB )) or resid 1001 through 1002)) selection = (chain 'C' and ((resid 389 through 391 and (name N or name CA or name C or name \ O or name CB )) or resid 392 through 398 or (resid 399 and (name N or name CA or \ name C or name O or name CB )) or resid 400 through 415 or (resid 416 and (name \ N or name CA or name C or name O or name CB )) or resid 417 through 466 or (res \ id 467 through 469 and (name N or name CA or name C or name O or name CB )) or r \ esid 470 through 546 or resid 567 through 569 or resid 571 through 581 or resid \ 587 through 618 or (resid 619 and (name N or name CA or name C or name O or name \ CB )) or resid 620 through 622 or resid 630 through 633 or (resid 634 and (name \ N or name CA or name C or name O or name CB )) or resid 635 through 687 or (res \ id 688 and (name N or name CA or name C or name O or name CB )) or resid 689 thr \ ough 691 or (resid 692 through 693 and (name N or name CA or name C or name O or \ name CB )) or resid 694 through 708 or (resid 709 and (name N or name CA or nam \ e C or name O or name CB )) or resid 710 through 815 or resid 1001 through 1002) \ ) selection = (chain 'D' and (resid 389 through 444 or (resid 445 and (name N or name CA or na \ me C or name O or name CB )) or resid 446 through 466 or (resid 467 through 469 \ and (name N or name CA or name C or name O or name CB )) or resid 470 through 50 \ 0 or (resid 501 through 502 and (name N or name CA or name C or name O or name C \ B )) or resid 508 through 545 or (resid 566 and (name N or name CA or name C or \ name O or name CB )) or resid 567 through 569 or resid 571 through 581 or resid \ 587 through 622 or resid 630 through 658 or (resid 659 and (name N or name CA or \ name C or name O or name CB )) or resid 660 through 664 or (resid 665 and (name \ N or name CA or name C or name O or name CB )) or resid 666 through 687 or (res \ id 688 and (name N or name CA or name C or name O or name CB )) or resid 689 thr \ ough 691 or (resid 692 through 693 and (name N or name CA or name C or name O or \ name CB )) or resid 694 through 705 or (resid 706 and (name N or name CA or nam \ e C or name O or name CB )) or resid 707 through 708 or (resid 709 and (name N o \ r name CA or name C or name O or name CB )) or resid 710 through 813 or (resid 8 \ 14 through 815 and (name N or name CA or name C or name O or name CB )) or resid \ 1001 through 1002)) } ncs_group { reference = (chain 'E' and (resid 5 through 209 or (resid 1201 and (name C1 or name C2 or na \ me C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 o \ r name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or name C3 \ 4 or name C35 or name C36 or name O11 or name O12 or name O13 or name O14 or nam \ e O21 or name O22 or name O31 or name O32 or name P or name C210 or name C211))) \ ) selection = (chain 'F' and (resid 5 through 209 or (resid 1301 and (name C1 or name C2 or na \ me C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 o \ r name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or name C3 \ 4 or name C35 or name C36 or name O11 or name O12 or name O13 or name O14 or nam \ e O21 or name O22 or name O31 or name O32 or name P or name C210 or name C211))) \ ) selection = (chain 'G' and (resid 5 through 209 or (resid 1201 and (name C1 or name C2 or na \ me C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 o \ r name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or name C3 \ 4 or name C35 or name C36 or name O11 or name O12 or name O13 or name O14 or nam \ e O21 or name O22 or name O31 or name O32 or name P or name C210 or name C211))) \ ) selection = (chain 'H' and (resid 5 through 209 or (resid 1301 and (name C1 or name C2 or na \ me C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 o \ r name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or name C3 \ 4 or name C35 or name C36 or name O11 or name O12 or name O13 or name O14 or nam \ e O21 or name O22 or name O31 or name O32 or name P or name C210 or name C211))) \ ) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 46.260 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 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 : 0.012 0.173 17829 Z= 0.803 Angle : 1.631 35.619 24111 Z= 1.158 Chirality : 0.127 2.127 2738 Planarity : 0.021 0.387 2952 Dihedral : 15.873 115.017 6181 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.03 % Favored : 96.88 % Rotamer: Outliers : 3.17 % Allowed : 4.63 % Favored : 92.20 % Cbeta Deviations : 0.92 % Peptide Plane: Cis-proline : 21.05 % 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: -0.44 (0.17), residues: 2211 helix: 0.68 (0.13), residues: 1356 sheet: -2.06 (0.35), residues: 167 loop : -1.69 (0.21), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.007 TRP D 602 HIS 0.015 0.004 HIS G 204 PHE 0.045 0.005 PHE B 567 TYR 0.030 0.006 TYR F 180 ARG 0.036 0.002 ARG B 595 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 302 time to evaluate : 1.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 788 VAL cc_start: 0.9138 (m) cc_final: 0.8928 (m) REVERT: D 398 GLU cc_start: -0.3761 (OUTLIER) cc_final: -0.4323 (mm-30) REVERT: D 781 SER cc_start: 0.8442 (OUTLIER) cc_final: 0.7929 (p) REVERT: F 70 GLU cc_start: 0.8742 (pt0) cc_final: 0.8514 (pp20) REVERT: F 128 HIS cc_start: 0.7736 (m-70) cc_final: 0.7397 (t-90) REVERT: G 10 MET cc_start: 0.9119 (tpp) cc_final: 0.8895 (tpp) REVERT: G 205 GLN cc_start: 0.9256 (tt0) cc_final: 0.8875 (tp40) REVERT: H 137 SER cc_start: 0.9307 (m) cc_final: 0.8839 (p) REVERT: H 184 PHE cc_start: 0.9127 (m-80) cc_final: 0.8909 (m-10) outliers start: 40 outliers final: 8 residues processed: 337 average time/residue: 0.3946 time to fit residues: 184.4182 Evaluate side-chains 164 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 154 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain C residue 734 LYS Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 502 LYS Chi-restraints excluded: chain D residue 659 LYS Chi-restraints excluded: chain D residue 781 SER Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 74 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 0.9990 chunk 167 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 173 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 128 optimal weight: 0.9990 chunk 200 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 GLN A 752 GLN ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 GLN C 431 HIS C 582 GLN E 204 HIS G 160 ASN G 204 HIS H 204 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17829 Z= 0.172 Angle : 0.567 10.063 24111 Z= 0.298 Chirality : 0.041 0.148 2738 Planarity : 0.004 0.045 2952 Dihedral : 10.639 114.444 2770 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.35 % Allowed : 11.61 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % 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: 1.36 (0.18), residues: 2211 helix: 2.17 (0.14), residues: 1346 sheet: -1.46 (0.37), residues: 179 loop : -1.02 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 667 HIS 0.006 0.001 HIS E 132 PHE 0.026 0.001 PHE C 542 TYR 0.015 0.001 TYR B 436 ARG 0.006 0.001 ARG H 74 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 190 time to evaluate : 1.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 803 MET cc_start: 0.8743 (mtm) cc_final: 0.8472 (mtm) REVERT: D 403 MET cc_start: 0.1058 (mpp) cc_final: 0.0846 (mpp) REVERT: F 128 HIS cc_start: 0.7803 (m-70) cc_final: 0.7444 (t-90) REVERT: G 102 ARG cc_start: 0.8810 (tmt-80) cc_final: 0.8584 (tpt170) REVERT: G 129 ARG cc_start: 0.6102 (OUTLIER) cc_final: 0.5827 (mtm180) REVERT: G 205 GLN cc_start: 0.9203 (tt0) cc_final: 0.8892 (tp40) REVERT: H 56 GLU cc_start: 0.9105 (pm20) cc_final: 0.8865 (mp0) REVERT: H 74 ARG cc_start: 0.9420 (ttp80) cc_final: 0.9128 (mtp-110) REVERT: H 149 ASN cc_start: 0.9277 (t0) cc_final: 0.9011 (m-40) REVERT: H 204 HIS cc_start: 0.8033 (OUTLIER) cc_final: 0.7520 (m90) outliers start: 30 outliers final: 13 residues processed: 214 average time/residue: 0.3420 time to fit residues: 107.2396 Evaluate side-chains 162 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 1.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain C residue 734 LYS Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 74 ARG Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 111 optimal weight: 8.9990 chunk 62 optimal weight: 0.6980 chunk 167 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 201 optimal weight: 3.9990 chunk 217 optimal weight: 5.9990 chunk 179 optimal weight: 4.9990 chunk 199 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 161 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 414 ASN E 132 HIS F 9 GLN ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN H 206 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17829 Z= 0.252 Angle : 0.561 9.719 24111 Z= 0.297 Chirality : 0.040 0.143 2738 Planarity : 0.004 0.041 2952 Dihedral : 9.844 96.112 2755 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.11 % Allowed : 12.84 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % 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: 1.69 (0.18), residues: 2211 helix: 2.37 (0.14), residues: 1365 sheet: -1.76 (0.37), residues: 149 loop : -0.76 (0.22), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 667 HIS 0.016 0.002 HIS G 204 PHE 0.025 0.001 PHE F 179 TYR 0.014 0.001 TYR A 643 ARG 0.005 0.001 ARG A 449 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 2.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 ASP cc_start: 0.9058 (m-30) cc_final: 0.8619 (m-30) REVERT: A 635 LEU cc_start: 0.9316 (tp) cc_final: 0.9068 (tt) REVERT: B 803 MET cc_start: 0.8813 (mtm) cc_final: 0.8580 (mtm) REVERT: C 761 LYS cc_start: 0.7397 (mmtt) cc_final: 0.6936 (tptt) REVERT: F 95 GLU cc_start: 0.8915 (tm-30) cc_final: 0.8651 (tp30) REVERT: F 128 HIS cc_start: 0.7852 (m-70) cc_final: 0.7503 (t-90) REVERT: F 204 HIS cc_start: 0.6344 (OUTLIER) cc_final: 0.5504 (m170) REVERT: G 56 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8270 (mm-30) REVERT: G 74 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8153 (ttp-170) REVERT: G 160 ASN cc_start: 0.9287 (m-40) cc_final: 0.9042 (m110) REVERT: G 205 GLN cc_start: 0.9208 (tt0) cc_final: 0.8884 (tp40) REVERT: H 56 GLU cc_start: 0.9108 (OUTLIER) cc_final: 0.8846 (mp0) REVERT: H 149 ASN cc_start: 0.9309 (t0) cc_final: 0.9089 (t0) outliers start: 27 outliers final: 14 residues processed: 172 average time/residue: 0.3306 time to fit residues: 85.3775 Evaluate side-chains 161 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 74 ARG Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 160 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 198 optimal weight: 0.7980 chunk 151 optimal weight: 0.7980 chunk 104 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 95 optimal weight: 0.8980 chunk 135 optimal weight: 0.9990 chunk 201 optimal weight: 6.9990 chunk 213 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 191 optimal weight: 7.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 160 ASN ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 HIS G 204 HIS H 206 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17829 Z= 0.151 Angle : 0.499 9.669 24111 Z= 0.261 Chirality : 0.038 0.133 2738 Planarity : 0.004 0.043 2952 Dihedral : 9.035 79.631 2751 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.05 % Allowed : 12.90 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % 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: 2.01 (0.18), residues: 2211 helix: 2.58 (0.14), residues: 1365 sheet: -1.58 (0.39), residues: 147 loop : -0.57 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 762 HIS 0.004 0.001 HIS E 204 PHE 0.018 0.001 PHE F 179 TYR 0.012 0.001 TYR B 519 ARG 0.006 0.000 ARG F 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 1.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 MET cc_start: 0.6080 (mpp) cc_final: 0.5385 (mmm) REVERT: A 459 MET cc_start: 0.1978 (mmm) cc_final: 0.1162 (mmt) REVERT: A 520 GLU cc_start: 0.8431 (mp0) cc_final: 0.8067 (mm-30) REVERT: A 581 MET cc_start: 0.9052 (mmt) cc_final: 0.8422 (mmm) REVERT: A 635 LEU cc_start: 0.9248 (tp) cc_final: 0.9045 (tt) REVERT: C 465 TYR cc_start: 0.3306 (m-10) cc_final: 0.3081 (m-10) REVERT: D 499 MET cc_start: -0.0539 (tpp) cc_final: -0.1463 (tpt) REVERT: D 717 MET cc_start: 0.6638 (mmp) cc_final: 0.6062 (mmp) REVERT: F 9 GLN cc_start: 0.8787 (mm110) cc_final: 0.8341 (mm-40) REVERT: F 78 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8586 (pttt) REVERT: F 128 HIS cc_start: 0.7831 (m-70) cc_final: 0.7452 (t-90) REVERT: F 204 HIS cc_start: 0.6042 (OUTLIER) cc_final: 0.5282 (m170) REVERT: G 56 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8260 (mm-30) REVERT: G 74 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.8248 (ttp-170) REVERT: G 160 ASN cc_start: 0.9282 (m-40) cc_final: 0.8973 (m110) REVERT: G 208 ARG cc_start: 0.7304 (tmm-80) cc_final: 0.6752 (mtt180) REVERT: H 56 GLU cc_start: 0.9122 (OUTLIER) cc_final: 0.8872 (mp0) REVERT: H 74 ARG cc_start: 0.9380 (ttp80) cc_final: 0.9167 (mtp-110) REVERT: H 149 ASN cc_start: 0.9275 (t0) cc_final: 0.9042 (t0) outliers start: 26 outliers final: 14 residues processed: 182 average time/residue: 0.3071 time to fit residues: 85.0653 Evaluate side-chains 167 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 74 ARG Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 160 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 177 optimal weight: 9.9990 chunk 121 optimal weight: 0.5980 chunk 3 optimal weight: 10.0000 chunk 159 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 182 optimal weight: 3.9990 chunk 147 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 109 optimal weight: 40.0000 chunk 191 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 HIS D 582 GLN B E 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 17829 Z= 0.511 Angle : 0.736 11.102 24111 Z= 0.387 Chirality : 0.044 0.165 2738 Planarity : 0.005 0.059 2952 Dihedral : 10.648 78.106 2750 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.99 % Allowed : 14.43 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % 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: 1.47 (0.18), residues: 2211 helix: 2.01 (0.14), residues: 1362 sheet: -1.78 (0.43), residues: 120 loop : -0.49 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 667 HIS 0.009 0.002 HIS G 204 PHE 0.023 0.002 PHE C 542 TYR 0.021 0.002 TYR A 420 ARG 0.005 0.001 ARG F 99 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 140 time to evaluate : 1.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 520 GLU cc_start: 0.8686 (mp0) cc_final: 0.8473 (mm-30) REVERT: A 581 MET cc_start: 0.9105 (mmt) cc_final: 0.8601 (mmm) REVERT: A 809 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8645 (tm-30) REVERT: C 686 MET cc_start: 0.1304 (mtp) cc_final: 0.0817 (tpt) REVERT: C 761 LYS cc_start: 0.7429 (mmtt) cc_final: 0.7072 (tptt) REVERT: F 9 GLN cc_start: 0.8877 (mm110) cc_final: 0.8439 (mm-40) REVERT: F 128 HIS cc_start: 0.7705 (m-70) cc_final: 0.7306 (t70) REVERT: F 204 HIS cc_start: 0.6625 (OUTLIER) cc_final: 0.5774 (m170) REVERT: G 56 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8470 (mm-30) REVERT: G 58 MET cc_start: 0.8848 (mmm) cc_final: 0.8347 (mmm) REVERT: G 160 ASN cc_start: 0.9295 (m-40) cc_final: 0.9002 (m110) REVERT: G 188 ILE cc_start: 0.9643 (mm) cc_final: 0.9363 (mt) REVERT: G 208 ARG cc_start: 0.7098 (tmm-80) cc_final: 0.6768 (mtt180) REVERT: H 9 GLN cc_start: 0.9189 (mt0) cc_final: 0.8791 (mm110) REVERT: H 149 ASN cc_start: 0.9410 (t0) cc_final: 0.9089 (t0) outliers start: 44 outliers final: 25 residues processed: 175 average time/residue: 0.3269 time to fit residues: 85.9335 Evaluate side-chains 150 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 2.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 781 SER Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 160 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 71 optimal weight: 10.0000 chunk 192 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 chunk 213 optimal weight: 1.9990 chunk 177 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 582 GLN B ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17829 Z= 0.267 Angle : 0.584 11.646 24111 Z= 0.304 Chirality : 0.040 0.204 2738 Planarity : 0.004 0.040 2952 Dihedral : 9.969 79.880 2746 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.40 % Allowed : 15.54 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % 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: 1.86 (0.18), residues: 2211 helix: 2.32 (0.14), residues: 1362 sheet: -1.62 (0.40), residues: 130 loop : -0.31 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP D 667 HIS 0.004 0.001 HIS G 204 PHE 0.019 0.001 PHE C 542 TYR 0.019 0.001 TYR A 420 ARG 0.005 0.000 ARG G 74 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 520 GLU cc_start: 0.8560 (mp0) cc_final: 0.8253 (mm-30) REVERT: A 581 MET cc_start: 0.9113 (mmt) cc_final: 0.8617 (mmm) REVERT: A 666 MET cc_start: 0.8525 (mpp) cc_final: 0.7645 (mpp) REVERT: A 809 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8604 (tm-30) REVERT: C 734 LYS cc_start: 0.3417 (tptt) cc_final: 0.2998 (pttm) REVERT: D 499 MET cc_start: -0.0857 (tpp) cc_final: -0.1662 (tpt) REVERT: F 9 GLN cc_start: 0.8885 (mm110) cc_final: 0.8331 (mm-40) REVERT: F 128 HIS cc_start: 0.7691 (m-70) cc_final: 0.7309 (t70) REVERT: F 204 HIS cc_start: 0.6572 (OUTLIER) cc_final: 0.5584 (m170) REVERT: G 56 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8457 (mm-30) REVERT: G 160 ASN cc_start: 0.9279 (m-40) cc_final: 0.8965 (m110) REVERT: G 204 HIS cc_start: 0.7492 (OUTLIER) cc_final: 0.7047 (m170) REVERT: G 208 ARG cc_start: 0.6892 (tmm-80) cc_final: 0.6643 (mtt180) REVERT: H 9 GLN cc_start: 0.9080 (mt0) cc_final: 0.8743 (mm110) REVERT: H 24 MET cc_start: 0.9469 (tpt) cc_final: 0.9212 (tpp) REVERT: H 74 ARG cc_start: 0.9374 (ttp80) cc_final: 0.9149 (mtp-110) outliers start: 34 outliers final: 22 residues processed: 166 average time/residue: 0.2999 time to fit residues: 76.0063 Evaluate side-chains 155 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 781 SER Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 160 ASN Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 206 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 156 optimal weight: 0.6980 chunk 120 optimal weight: 9.9990 chunk 179 optimal weight: 3.9990 chunk 119 optimal weight: 40.0000 chunk 213 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 129 optimal weight: 0.7980 chunk 98 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.4720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17829 Z= 0.158 Angle : 0.538 9.884 24111 Z= 0.278 Chirality : 0.039 0.160 2738 Planarity : 0.004 0.040 2952 Dihedral : 8.897 79.566 2746 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.76 % Allowed : 16.25 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % 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: 2.23 (0.18), residues: 2211 helix: 2.63 (0.14), residues: 1361 sheet: -1.42 (0.41), residues: 123 loop : -0.22 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP D 667 HIS 0.003 0.001 HIS E 204 PHE 0.017 0.001 PHE C 542 TYR 0.012 0.001 TYR A 420 ARG 0.004 0.000 ARG A 449 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 2.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 MET cc_start: 0.2356 (mmm) cc_final: 0.1544 (mmp) REVERT: A 520 GLU cc_start: 0.8469 (mp0) cc_final: 0.8144 (mm-30) REVERT: C 465 TYR cc_start: 0.3089 (m-10) cc_final: 0.2862 (m-10) REVERT: C 734 LYS cc_start: 0.3721 (tptt) cc_final: 0.3307 (pttm) REVERT: C 761 LYS cc_start: 0.7130 (mmtt) cc_final: 0.6645 (tppt) REVERT: D 499 MET cc_start: -0.0903 (tpp) cc_final: -0.1489 (tpt) REVERT: D 616 LEU cc_start: 0.9536 (tp) cc_final: 0.9295 (tp) REVERT: F 9 GLN cc_start: 0.8936 (mm110) cc_final: 0.8452 (mm-40) REVERT: F 128 HIS cc_start: 0.7654 (m-70) cc_final: 0.7282 (t70) REVERT: F 204 HIS cc_start: 0.6218 (OUTLIER) cc_final: 0.5324 (m170) REVERT: G 56 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8390 (mm-30) REVERT: G 58 MET cc_start: 0.8941 (mmm) cc_final: 0.8703 (tpp) REVERT: G 74 ARG cc_start: 0.9146 (ttp80) cc_final: 0.8437 (ttp-110) REVERT: G 204 HIS cc_start: 0.7631 (OUTLIER) cc_final: 0.7255 (m170) REVERT: G 208 ARG cc_start: 0.6707 (tmm-80) cc_final: 0.6471 (mtt180) REVERT: H 9 GLN cc_start: 0.9087 (mt0) cc_final: 0.8716 (mm-40) outliers start: 23 outliers final: 17 residues processed: 170 average time/residue: 0.3036 time to fit residues: 80.5932 Evaluate side-chains 161 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 150 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 131 optimal weight: 1.9990 chunk 85 optimal weight: 20.0000 chunk 127 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 135 optimal weight: 0.9990 chunk 145 optimal weight: 8.9990 chunk 105 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 193 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 206 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.4913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17829 Z= 0.306 Angle : 0.600 10.619 24111 Z= 0.313 Chirality : 0.041 0.202 2738 Planarity : 0.004 0.052 2952 Dihedral : 9.216 78.800 2746 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.64 % Allowed : 16.13 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % 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: 2.04 (0.18), residues: 2211 helix: 2.42 (0.14), residues: 1359 sheet: -1.37 (0.39), residues: 146 loop : -0.14 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP D 667 HIS 0.003 0.001 HIS E 132 PHE 0.019 0.001 PHE C 542 TYR 0.019 0.001 TYR A 420 ARG 0.011 0.001 ARG H 74 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 2.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 MET cc_start: 0.2596 (mmm) cc_final: 0.1720 (mmp) REVERT: A 520 GLU cc_start: 0.8584 (mp0) cc_final: 0.8347 (mm-30) REVERT: A 581 MET cc_start: 0.9093 (mmt) cc_final: 0.8708 (mmm) REVERT: A 809 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8612 (tm-30) REVERT: C 734 LYS cc_start: 0.3356 (tptt) cc_final: 0.2975 (pttm) REVERT: C 761 LYS cc_start: 0.7489 (mmtt) cc_final: 0.6864 (tptt) REVERT: D 499 MET cc_start: -0.0777 (tpp) cc_final: -0.1454 (tpt) REVERT: F 9 GLN cc_start: 0.8956 (mm110) cc_final: 0.8434 (mm-40) REVERT: F 128 HIS cc_start: 0.7701 (m-70) cc_final: 0.7313 (t70) REVERT: F 204 HIS cc_start: 0.6512 (OUTLIER) cc_final: 0.5389 (m170) REVERT: G 56 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8444 (mm-30) REVERT: G 160 ASN cc_start: 0.9235 (m-40) cc_final: 0.9005 (m110) REVERT: H 9 GLN cc_start: 0.9091 (mt0) cc_final: 0.8725 (mm110) outliers start: 38 outliers final: 28 residues processed: 165 average time/residue: 0.3156 time to fit residues: 81.3933 Evaluate side-chains 159 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 2.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 781 SER Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 717 MET Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 160 ASN Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 204 optimal weight: 7.9990 chunk 186 optimal weight: 5.9990 chunk 198 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 187 optimal weight: 10.0000 chunk 197 optimal weight: 8.9990 chunk 130 optimal weight: 8.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 582 GLN ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.5071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17829 Z= 0.275 Angle : 0.597 10.564 24111 Z= 0.308 Chirality : 0.040 0.174 2738 Planarity : 0.004 0.061 2952 Dihedral : 8.960 80.017 2746 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.29 % Allowed : 16.36 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % 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: 2.08 (0.18), residues: 2211 helix: 2.45 (0.14), residues: 1359 sheet: -1.37 (0.39), residues: 146 loop : -0.12 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP D 667 HIS 0.003 0.001 HIS H 198 PHE 0.019 0.001 PHE C 542 TYR 0.016 0.001 TYR B 420 ARG 0.007 0.001 ARG H 74 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 1.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 MET cc_start: 0.2544 (mmm) cc_final: 0.1659 (mmp) REVERT: A 520 GLU cc_start: 0.8540 (mp0) cc_final: 0.8306 (mm-30) REVERT: A 809 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8635 (tm-30) REVERT: C 465 TYR cc_start: 0.3044 (m-10) cc_final: 0.2837 (m-10) REVERT: C 717 MET cc_start: 0.7201 (pmm) cc_final: 0.6766 (pmm) REVERT: C 734 LYS cc_start: 0.3358 (tptt) cc_final: 0.3025 (pttm) REVERT: D 499 MET cc_start: -0.0625 (tpp) cc_final: -0.1181 (tpt) REVERT: F 9 GLN cc_start: 0.8949 (mm110) cc_final: 0.8425 (mm-40) REVERT: F 128 HIS cc_start: 0.7673 (m-70) cc_final: 0.7314 (t70) REVERT: F 204 HIS cc_start: 0.6477 (OUTLIER) cc_final: 0.5413 (m170) REVERT: G 56 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8420 (mm-30) REVERT: G 160 ASN cc_start: 0.9220 (m-40) cc_final: 0.8973 (m110) REVERT: H 9 GLN cc_start: 0.9066 (mt0) cc_final: 0.8713 (mm110) REVERT: H 149 ASN cc_start: 0.9141 (t0) cc_final: 0.8619 (m-40) outliers start: 32 outliers final: 30 residues processed: 159 average time/residue: 0.3119 time to fit residues: 77.0259 Evaluate side-chains 163 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 781 SER Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 748 LYS Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 670 MET Chi-restraints excluded: chain D residue 717 MET Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 160 ASN Chi-restraints excluded: chain H residue 198 HIS Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 209 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 145 optimal weight: 0.0050 chunk 220 optimal weight: 1.9990 chunk 202 optimal weight: 2.9990 chunk 175 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 107 optimal weight: 0.0020 chunk 139 optimal weight: 0.9990 overall best weight: 0.8008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 206 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.5149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17829 Z= 0.164 Angle : 0.577 11.610 24111 Z= 0.290 Chirality : 0.039 0.173 2738 Planarity : 0.004 0.068 2952 Dihedral : 8.495 80.512 2746 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.58 % Allowed : 17.42 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % 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: 2.23 (0.18), residues: 2211 helix: 2.58 (0.14), residues: 1356 sheet: -1.33 (0.39), residues: 154 loop : -0.04 (0.24), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.001 TRP D 667 HIS 0.003 0.001 HIS E 204 PHE 0.018 0.001 PHE F 179 TYR 0.013 0.001 TYR A 643 ARG 0.008 0.000 ARG A 481 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 2.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 MET cc_start: 0.2318 (mmm) cc_final: 0.1525 (mmp) REVERT: A 520 GLU cc_start: 0.8479 (mp0) cc_final: 0.8144 (mm-30) REVERT: A 581 MET cc_start: 0.9078 (mmt) cc_final: 0.8555 (mmm) REVERT: C 459 MET cc_start: 0.6449 (mpp) cc_final: 0.5845 (mpp) REVERT: C 465 TYR cc_start: 0.3031 (m-10) cc_final: 0.2809 (m-10) REVERT: C 717 MET cc_start: 0.7191 (pmm) cc_final: 0.6741 (pmm) REVERT: C 734 LYS cc_start: 0.3519 (tptt) cc_final: 0.3146 (pttm) REVERT: D 403 MET cc_start: 0.3362 (mpp) cc_final: 0.2730 (mpp) REVERT: D 499 MET cc_start: -0.0826 (tpp) cc_final: -0.1266 (tpt) REVERT: F 9 GLN cc_start: 0.8824 (mm110) cc_final: 0.8460 (mm-40) REVERT: F 128 HIS cc_start: 0.7662 (m-70) cc_final: 0.7307 (t70) REVERT: F 204 HIS cc_start: 0.6273 (OUTLIER) cc_final: 0.5339 (m170) REVERT: G 56 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8367 (mm-30) REVERT: G 74 ARG cc_start: 0.9167 (ttp80) cc_final: 0.8490 (ttp-110) REVERT: G 160 ASN cc_start: 0.9192 (m-40) cc_final: 0.8939 (m110) REVERT: H 9 GLN cc_start: 0.8946 (mt0) cc_final: 0.8615 (mm-40) outliers start: 20 outliers final: 17 residues processed: 157 average time/residue: 0.2933 time to fit residues: 71.3920 Evaluate side-chains 155 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 2.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 717 MET Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 161 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 48 optimal weight: 8.9990 chunk 175 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 180 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 154 optimal weight: 7.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.126346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.077941 restraints weight = 149601.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.080343 restraints weight = 48381.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.081363 restraints weight = 27724.981| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3250 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3250 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.5212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17829 Z= 0.219 Angle : 0.598 12.095 24111 Z= 0.302 Chirality : 0.040 0.212 2738 Planarity : 0.004 0.059 2952 Dihedral : 8.479 80.027 2746 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.58 % Allowed : 17.65 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % 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: 2.20 (0.18), residues: 2211 helix: 2.53 (0.14), residues: 1359 sheet: -1.28 (0.38), residues: 159 loop : -0.01 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP D 667 HIS 0.003 0.001 HIS E 204 PHE 0.018 0.001 PHE C 542 TYR 0.014 0.001 TYR A 420 ARG 0.009 0.000 ARG A 657 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3174.90 seconds wall clock time: 59 minutes 38.44 seconds (3578.44 seconds total)