Starting phenix.real_space_refine on Tue Apr 9 21:32:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3w_17397/04_2024/8p3w_17397_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3w_17397/04_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_17397/04_2024/8p3w_17397.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3w_17397/04_2024/8p3w_17397.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3w_17397/04_2024/8p3w_17397_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3w_17397/04_2024/8p3w_17397_neut_updated.pdb" } 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 Residue "A GLU 427": "OE1" <-> "OE2" Residue "A ARG 449": "NH1" <-> "NH2" Residue "A GLU 482": "OE1" <-> "OE2" Residue "A ARG 590": "NH1" <-> "NH2" Residue "A TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 711": "NH1" <-> "NH2" Residue "A GLU 751": "OE1" <-> "OE2" Residue "B GLU 423": "OE1" <-> "OE2" Residue "B ARG 449": "NH1" <-> "NH2" Residue "B GLU 482": "OE1" <-> "OE2" Residue "B GLU 483": "OE1" <-> "OE2" Residue "B PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 633": "OE1" <-> "OE2" Residue "B GLU 684": "OE1" <-> "OE2" Residue "C GLU 418": "OE1" <-> "OE2" Residue "C GLU 427": "OE1" <-> "OE2" Residue "C ARG 449": "NH1" <-> "NH2" Residue "C GLU 482": "OE1" <-> "OE2" Residue "C ARG 590": "NH1" <-> "NH2" Residue "C GLU 701": "OE1" <-> "OE2" Residue "D PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 427": "OE1" <-> "OE2" Residue "D ARG 449": "NH1" <-> "NH2" Residue "D GLU 482": "OE1" <-> "OE2" Residue "D GLU 483": "OE1" <-> "OE2" Residue "D PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 690": "NH1" <-> "NH2" Residue "D GLU 701": "OE1" <-> "OE2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E GLU 70": "OE1" <-> "OE2" Residue "F GLU 56": "OE1" <-> "OE2" Residue "F GLU 126": "OE1" <-> "OE2" Residue "F GLU 190": "OE1" <-> "OE2" Residue "G GLU 55": "OE1" <-> "OE2" Residue "G GLU 70": "OE1" <-> "OE2" Residue "H GLU 56": "OE1" <-> "OE2" Residue "H GLU 126": "OE1" <-> "OE2" Residue "H GLU 190": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 15.12, 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.66 Conformation dependent library (CDL) restraints added in 5.3 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... running ksdssp... Secondary structure from input PDB file: 87 helices and 22 sheets defined 55.8% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.15 Creating SS restraints... Processing helix chain 'A' and resid 408 through 410 No H-bonds generated for 'chain 'A' and resid 408 through 410' Processing helix chain 'A' and resid 413 through 416 Processing helix chain 'A' and resid 420 through 432 Processing helix chain 'A' and resid 458 through 465 Processing helix chain 'A' and resid 479 through 482 No H-bonds generated for 'chain 'A' and resid 479 through 482' Processing helix chain 'A' and resid 512 through 514 No H-bonds generated for 'chain 'A' and resid 512 through 514' Processing helix chain 'A' and resid 519 through 541 Processing helix chain 'A' and resid 569 through 580 Processing helix chain 'A' and resid 592 through 625 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 632 through 637 Processing helix chain 'A' and resid 650 through 656 Processing helix chain 'A' and resid 661 through 672 Processing helix chain 'A' and resid 682 through 691 Processing helix chain 'A' and resid 702 through 709 Processing helix chain 'A' and resid 739 through 751 Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 785 through 813 removed outlier: 3.797A pdb=" N ALA A 789 " --> pdb=" O SER A 786 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N GLY A 790 " --> pdb=" O ASN A 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 410 No H-bonds generated for 'chain 'B' and resid 408 through 410' Processing helix chain 'B' and resid 414 through 416 No H-bonds generated for 'chain 'B' and resid 414 through 416' Processing helix chain 'B' and resid 420 through 432 Processing helix chain 'B' and resid 458 through 464 Processing helix chain 'B' and resid 479 through 482 No H-bonds generated for 'chain 'B' and resid 479 through 482' Processing helix chain 'B' and resid 512 through 514 No H-bonds generated for 'chain 'B' and resid 512 through 514' Processing helix chain 'B' and resid 519 through 541 Processing helix chain 'B' and resid 569 through 580 Processing helix chain 'B' and resid 592 through 622 Processing helix chain 'B' and resid 632 through 637 Processing helix chain 'B' and resid 650 through 656 Processing helix chain 'B' and resid 661 through 672 removed outlier: 3.618A pdb=" N SER B 672 " --> pdb=" O THR B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 691 Processing helix chain 'B' and resid 702 through 710 Processing helix chain 'B' and resid 739 through 751 Processing helix chain 'B' and resid 754 through 763 Processing helix chain 'B' and resid 785 through 814 removed outlier: 3.565A pdb=" N ALA B 789 " --> pdb=" O SER B 786 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N GLY B 790 " --> pdb=" O ASN B 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 410 No H-bonds generated for 'chain 'C' and resid 408 through 410' Processing helix chain 'C' and resid 414 through 416 No H-bonds generated for 'chain 'C' and resid 414 through 416' Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 458 through 465 Processing helix chain 'C' and resid 479 through 482 No H-bonds generated for 'chain 'C' and resid 479 through 482' Processing helix chain 'C' and resid 512 through 514 No H-bonds generated for 'chain 'C' and resid 512 through 514' Processing helix chain 'C' and resid 519 through 541 Processing helix chain 'C' and resid 569 through 580 Processing helix chain 'C' and resid 592 through 621 Processing helix chain 'C' and resid 632 through 637 Processing helix chain 'C' and resid 650 through 656 Processing helix chain 'C' and resid 661 through 671 Processing helix chain 'C' and resid 682 through 690 Processing helix chain 'C' and resid 702 through 710 Processing helix chain 'C' and resid 739 through 751 Processing helix chain 'C' and resid 754 through 763 Processing helix chain 'C' and resid 785 through 813 removed outlier: 3.828A pdb=" N ALA C 789 " --> pdb=" O SER C 786 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N GLY C 790 " --> pdb=" O ASN C 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 416 Processing helix chain 'D' and resid 420 through 432 Processing helix chain 'D' and resid 458 through 465 Processing helix chain 'D' and resid 479 through 482 No H-bonds generated for 'chain 'D' and resid 479 through 482' Processing helix chain 'D' and resid 512 through 514 No H-bonds generated for 'chain 'D' and resid 512 through 514' Processing helix chain 'D' and resid 519 through 541 Processing helix chain 'D' and resid 569 through 580 Processing helix chain 'D' and resid 592 through 621 Processing helix chain 'D' and resid 632 through 637 Processing helix chain 'D' and resid 650 through 656 Processing helix chain 'D' and resid 661 through 672 removed outlier: 3.599A pdb=" N SER D 672 " --> pdb=" O THR D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 691 Processing helix chain 'D' and resid 702 through 710 Processing helix chain 'D' and resid 739 through 751 Processing helix chain 'D' and resid 754 through 763 Processing helix chain 'D' and resid 785 through 814 removed outlier: 3.526A pdb=" N ALA D 789 " --> pdb=" O SER D 786 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLY D 790 " --> pdb=" O ASN D 787 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 29 Processing helix chain 'E' and resid 93 through 103 Processing helix chain 'E' and resid 106 through 127 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 133 through 161 Processing helix chain 'E' and resid 177 through 208 Processing helix chain 'F' and resid 6 through 29 Processing helix chain 'F' and resid 93 through 104 Processing helix chain 'F' and resid 106 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 161 removed outlier: 3.969A pdb=" N ALA F 161 " --> pdb=" O SER F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 208 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 29 Processing helix chain 'G' and resid 93 through 103 Processing helix chain 'G' and resid 106 through 127 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 133 through 161 Processing helix chain 'G' and resid 177 through 208 Processing helix chain 'H' and resid 6 through 29 Processing helix chain 'H' and resid 93 through 104 Processing helix chain 'H' and resid 106 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 161 removed outlier: 4.028A pdb=" N ALA H 161 " --> pdb=" O SER H 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 208 removed outlier: 3.544A pdb=" N ARG H 208 " --> pdb=" O HIS H 204 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 390 through 395 removed outlier: 6.742A pdb=" N SER A 435 " --> pdb=" O TYR A 391 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N VAL A 393 " --> pdb=" O SER A 435 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ARG A 437 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N THR A 395 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLU A 439 " --> pdb=" O THR A 395 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 447 through 450 removed outlier: 3.702A pdb=" N ALA A 448 " --> pdb=" O ASN A 457 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA A 455 " --> pdb=" O ASP A 450 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 485 through 487 Processing sheet with id= D, 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= E, first strand: chain 'A' and resid 716 through 719 removed outlier: 4.173A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N LYS A 501 " --> pdb=" O TYR A 696 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N TYR A 696 " --> pdb=" O LYS A 501 " (cutoff:3.500A) 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) Processing sheet with id= F, first strand: chain 'B' and resid 391 through 395 Processing sheet with id= G, first strand: chain 'B' and resid 485 through 487 Processing sheet with id= H, 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= I, first strand: chain 'B' and resid 716 through 719 removed outlier: 4.230A pdb=" N ILE B 498 " --> pdb=" O VAL B 719 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LYS B 501 " --> pdb=" O TYR B 696 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N TYR B 696 " --> pdb=" O LYS B 501 " (cutoff:3.500A) 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) Processing sheet with id= J, first strand: chain 'C' and resid 390 through 395 removed outlier: 6.772A pdb=" N SER C 435 " --> pdb=" O TYR C 391 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N VAL C 393 " --> pdb=" O SER C 435 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ARG C 437 " --> pdb=" O VAL C 393 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N THR C 395 " --> pdb=" O ARG C 437 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLU C 439 " --> pdb=" O THR C 395 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 447 through 450 removed outlier: 3.806A pdb=" N ALA C 448 " --> pdb=" O ASN C 457 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA C 455 " --> pdb=" O ASP C 450 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 485 through 487 Processing sheet with id= M, 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= N, first strand: chain 'C' and resid 717 through 719 removed outlier: 4.256A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) 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) Processing sheet with id= O, first strand: chain 'D' and resid 391 through 395 Processing sheet with id= P, first strand: chain 'D' and resid 485 through 487 Processing sheet with id= Q, first strand: chain 'D' and resid 716 through 719 removed outlier: 4.086A pdb=" N ILE D 498 " --> pdb=" O VAL D 719 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LYS D 501 " --> pdb=" O TYR D 696 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N TYR D 696 " --> pdb=" O LYS D 501 " (cutoff:3.500A) 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) Processing sheet with id= R, first strand: chain 'D' and resid 490 through 494 removed outlier: 6.580A pdb=" N TYR D 728 " --> pdb=" O PHE D 491 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N SER D 493 " --> pdb=" O LYS D 726 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LYS D 726 " --> pdb=" O SER D 493 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 59 through 61 Processing sheet with id= T, first strand: chain 'F' and resid 173 through 175 Processing sheet with id= U, first strand: chain 'G' and resid 59 through 61 Processing sheet with id= V, first strand: chain 'H' and resid 173 through 175 995 hydrogen bonds defined for protein. 2505 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: 5.38 Time building geometry restraints manager: 7.88 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: 74.87 - 86.85: 1 86.85 - 98.82: 10 98.82 - 110.80: 5900 110.80 - 122.77: 15511 122.77 - 134.75: 2689 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: 87 2.57 - 3.15: 15057 3.15 - 3.74: 26857 3.74 - 4.32: 39111 4.32 - 4.90: 63502 Nonbonded interactions: 144614 Sorted by model distance: nonbonded pdb=" N SER A 725 " pdb=" O LYS D 659 " model vdw 1.988 2.520 nonbonded pdb=" O GLY A 720 " pdb=" NZ LYS D 665 " model vdw 2.051 2.520 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 2.520 nonbonded pdb=" N GLU E 55 " pdb=" OE1 GLU E 55 " model vdw 2.304 2.520 ... (remaining 144609 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.690 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 56.620 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.140 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: 0.020 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.690 ------------------------------------------------------------------------------- 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= 0.801 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 fitting. rotamer outliers: 40 poor density : 302 time to evaluate : 1.784 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: 0.3922 time to fit residues: 183.3044 Evaluate side-chains 164 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 154 time to evaluate : 2.059 ------------------------------------------------------------------------------- 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: 0.9980 chunk 167 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 112 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 173 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 128 optimal weight: 0.9990 chunk 200 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 H 204 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2613 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= 0.179 Angle : 0.558 9.973 24111 Z= 0.300 Chirality : 0.040 0.165 2738 Planarity : 0.005 0.043 2952 Dihedral : 10.575 114.681 2770 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.58 % Allowed : 11.61 % Favored : 85.81 % 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: 0.86 (0.17), residues: 2211 helix: 1.66 (0.14), residues: 1344 sheet: -1.70 (0.37), residues: 155 loop : -0.97 (0.21), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 667 HIS 0.004 0.001 HIS E 132 PHE 0.024 0.001 PHE C 542 TYR 0.014 0.001 TYR C 519 ARG 0.007 0.001 ARG C 711 *********************** 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 214 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 184 time to evaluate : 2.021 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: C 405 LYS cc_start: 0.7235 (mtmt) cc_final: 0.6996 (ptpt) REVERT: F 128 HIS cc_start: 0.7737 (m-70) cc_final: 0.7419 (t-90) REVERT: G 205 GLN cc_start: 0.9295 (tt0) cc_final: 0.8898 (tp-100) REVERT: H 56 GLU cc_start: 0.9100 (pm20) cc_final: 0.8867 (mp0) REVERT: H 137 SER cc_start: 0.9079 (m) cc_final: 0.8775 (p) REVERT: H 149 ASN cc_start: 0.8947 (t0) cc_final: 0.8585 (m-40) REVERT: H 204 HIS cc_start: 0.8045 (OUTLIER) cc_final: 0.7528 (m90) outliers start: 30 outliers final: 12 residues processed: 207 average time/residue: 0.3249 time to fit residues: 100.7191 Evaluate side-chains 157 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 144 time to evaluate : 2.059 ------------------------------------------------------------------------------- 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 734 LYS Chi-restraints excluded: chain C residue 756 ASP Chi-restraints excluded: chain D residue 443 ASP Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 129 ARG 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: 20.0000 chunk 62 optimal weight: 0.0060 chunk 167 optimal weight: 5.9990 chunk 136 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 201 optimal weight: 5.9990 chunk 217 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 161 optimal weight: 4.9990 overall best weight: 3.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 HIS B 414 ASN ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 HIS H 206 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17829 Z= 0.344 Angle : 0.607 9.267 24111 Z= 0.325 Chirality : 0.041 0.147 2738 Planarity : 0.005 0.045 2952 Dihedral : 10.301 95.594 2751 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.52 % Allowed : 13.67 % Favored : 83.81 % 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: 0.90 (0.17), residues: 2211 helix: 1.54 (0.14), residues: 1344 sheet: -1.51 (0.39), residues: 148 loop : -0.68 (0.21), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 667 HIS 0.027 0.003 HIS E 204 PHE 0.023 0.002 PHE C 542 TYR 0.017 0.002 TYR A 420 ARG 0.004 0.001 ARG C 711 *********************** 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 188 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 159 time to evaluate : 1.823 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: A 515 ASP cc_start: 0.9118 (m-30) cc_final: 0.8707 (m-30) REVERT: A 581 MET cc_start: 0.8984 (mmt) cc_final: 0.8570 (mmm) REVERT: B 666 MET cc_start: -0.2718 (mmm) cc_final: -0.2977 (mmm) REVERT: B 803 MET cc_start: 0.8852 (mtm) cc_final: 0.8651 (mtm) REVERT: C 405 LYS cc_start: 0.7203 (mtmt) cc_final: 0.6980 (ptpt) REVERT: C 459 MET cc_start: 0.4390 (mtm) cc_final: 0.4079 (ttm) REVERT: F 95 GLU cc_start: 0.8993 (tm-30) cc_final: 0.8764 (tp30) REVERT: F 128 HIS cc_start: 0.7867 (m-70) cc_final: 0.7513 (t-90) REVERT: F 204 HIS cc_start: 0.6703 (OUTLIER) cc_final: 0.5852 (m170) REVERT: G 56 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8279 (mm-30) REVERT: G 58 MET cc_start: 0.8913 (mmm) cc_final: 0.8534 (mmt) REVERT: G 205 GLN cc_start: 0.9251 (tt0) cc_final: 0.8916 (tp40) REVERT: H 56 GLU cc_start: 0.9034 (pm20) cc_final: 0.8790 (mp0) REVERT: H 137 SER cc_start: 0.9249 (m) cc_final: 0.8981 (p) REVERT: H 149 ASN cc_start: 0.9018 (t0) cc_final: 0.8718 (t0) outliers start: 29 outliers final: 17 residues processed: 180 average time/residue: 0.3334 time to fit residues: 90.5114 Evaluate side-chains 159 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 141 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain D residue 443 ASP Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 150 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 198 optimal weight: 6.9990 chunk 151 optimal weight: 0.9980 chunk 104 optimal weight: 20.0000 chunk 22 optimal weight: 0.0870 chunk 95 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 201 optimal weight: 4.9990 chunk 213 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 191 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 HIS ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN H 206 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17829 Z= 0.169 Angle : 0.503 9.209 24111 Z= 0.269 Chirality : 0.038 0.155 2738 Planarity : 0.004 0.042 2952 Dihedral : 9.399 79.281 2747 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.35 % Allowed : 14.84 % Favored : 82.82 % 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: 1.16 (0.18), residues: 2211 helix: 1.70 (0.14), residues: 1354 sheet: -1.34 (0.41), residues: 142 loop : -0.53 (0.21), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 667 HIS 0.005 0.001 HIS H 204 PHE 0.020 0.001 PHE B 491 TYR 0.015 0.001 TYR B 519 ARG 0.005 0.000 ARG A 449 *********************** 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 fitting. rotamer outliers: 27 poor density : 161 time to evaluate : 1.821 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: 0.6961 (mpp) cc_final: 0.6439 (mmm) REVERT: A 515 ASP cc_start: 0.9075 (m-30) cc_final: 0.8634 (m-30) REVERT: B 666 MET cc_start: -0.2553 (mmm) cc_final: -0.2767 (mmm) REVERT: C 405 LYS cc_start: 0.7152 (mtmt) cc_final: 0.6922 (ptpt) REVERT: C 459 MET cc_start: 0.4315 (mtm) cc_final: 0.4103 (ttm) REVERT: C 670 MET cc_start: -0.2032 (ttt) cc_final: -0.2237 (tpp) REVERT: F 9 GLN cc_start: 0.8501 (mm-40) cc_final: 0.8062 (mm-40) REVERT: F 78 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8552 (pttt) REVERT: F 95 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8703 (tp30) REVERT: F 128 HIS cc_start: 0.7865 (m-70) cc_final: 0.7501 (t70) REVERT: F 135 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.8188 (tp) REVERT: F 204 HIS cc_start: 0.6441 (OUTLIER) cc_final: 0.5220 (m170) REVERT: G 56 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8335 (mm-30) REVERT: G 69 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8717 (tp) REVERT: G 205 GLN cc_start: 0.9255 (tt0) cc_final: 0.8913 (tp40) REVERT: H 56 GLU cc_start: 0.9086 (pm20) cc_final: 0.8829 (mp0) REVERT: H 74 ARG cc_start: 0.9369 (ttp80) cc_final: 0.9154 (mtp-110) REVERT: H 137 SER cc_start: 0.9198 (m) cc_final: 0.8994 (p) REVERT: H 149 ASN cc_start: 0.9014 (t0) cc_final: 0.8679 (m-40) outliers start: 27 outliers final: 19 residues processed: 183 average time/residue: 0.3275 time to fit residues: 89.6701 Evaluate side-chains 170 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 147 time to evaluate : 2.012 ------------------------------------------------------------------------------- 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 781 SER Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 787 ASN 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 E residue 160 ASN Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 150 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 177 optimal weight: 8.9990 chunk 121 optimal weight: 0.0670 chunk 3 optimal weight: 9.9990 chunk 159 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 182 optimal weight: 0.6980 chunk 147 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 109 optimal weight: 30.0000 chunk 191 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 overall best weight: 4.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 17829 Z= 0.407 Angle : 0.642 11.152 24111 Z= 0.340 Chirality : 0.042 0.162 2738 Planarity : 0.005 0.044 2952 Dihedral : 10.314 87.099 2746 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.34 % Allowed : 14.90 % Favored : 81.76 % 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: 0.92 (0.18), residues: 2211 helix: 1.44 (0.14), residues: 1340 sheet: -1.49 (0.40), residues: 138 loop : -0.40 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 667 HIS 0.008 0.001 HIS F 82 PHE 0.027 0.002 PHE B 542 TYR 0.022 0.002 TYR A 420 ARG 0.004 0.001 ARG C 481 *********************** 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 183 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 140 time to evaluate : 1.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 MET cc_start: 0.9080 (mmt) cc_final: 0.8679 (mmm) REVERT: C 391 TYR cc_start: 0.5851 (m-80) cc_final: 0.5524 (m-80) REVERT: C 405 LYS cc_start: 0.7124 (mtmt) cc_final: 0.6846 (ptpt) REVERT: C 459 MET cc_start: 0.4426 (mtm) cc_final: 0.4161 (ttm) REVERT: C 670 MET cc_start: -0.1715 (ttt) cc_final: -0.2100 (tpp) REVERT: C 734 LYS cc_start: 0.3781 (tptt) cc_final: 0.3405 (pttm) REVERT: C 761 LYS cc_start: 0.7495 (mmtt) cc_final: 0.7258 (tptt) REVERT: D 499 MET cc_start: 0.0175 (tpp) cc_final: -0.0636 (tpt) REVERT: F 128 HIS cc_start: 0.7706 (m-70) cc_final: 0.7342 (t70) REVERT: F 204 HIS cc_start: 0.6811 (OUTLIER) cc_final: 0.5718 (m170) REVERT: G 56 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8426 (mm-30) REVERT: G 205 GLN cc_start: 0.9261 (tt0) cc_final: 0.8872 (tp40) REVERT: H 74 ARG cc_start: 0.9339 (ttp80) cc_final: 0.9076 (ttm110) REVERT: H 137 SER cc_start: 0.9310 (m) cc_final: 0.9062 (p) REVERT: H 149 ASN cc_start: 0.9076 (t0) cc_final: 0.8791 (t0) outliers start: 43 outliers final: 30 residues processed: 179 average time/residue: 0.3062 time to fit residues: 82.9504 Evaluate side-chains 163 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 132 time to evaluate : 1.891 ------------------------------------------------------------------------------- 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 781 SER Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 781 SER Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain C residue 486 ASP 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 756 ASP Chi-restraints excluded: chain D residue 443 ASP Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 754 VAL Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 158 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 135 ILE Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 129 ARG 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 204 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 71 optimal weight: 20.0000 chunk 192 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 125 optimal weight: 30.0000 chunk 52 optimal weight: 0.8980 chunk 213 optimal weight: 1.9990 chunk 177 optimal weight: 8.9990 chunk 99 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 70 optimal weight: 9.9990 chunk 112 optimal weight: 4.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 705 ASN E 160 ASN ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 17829 Z= 0.293 Angle : 0.565 12.507 24111 Z= 0.300 Chirality : 0.040 0.214 2738 Planarity : 0.005 0.044 2952 Dihedral : 10.019 79.635 2746 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.17 % Allowed : 15.31 % Favored : 81.52 % 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: 1.06 (0.18), residues: 2211 helix: 1.56 (0.14), residues: 1343 sheet: -1.58 (0.42), residues: 127 loop : -0.37 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 667 HIS 0.004 0.001 HIS H 198 PHE 0.022 0.001 PHE B 542 TYR 0.021 0.001 TYR B 519 ARG 0.004 0.000 ARG A 657 *********************** 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 178 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 138 time to evaluate : 2.015 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 581 MET cc_start: 0.9093 (mmt) cc_final: 0.8695 (mmm) REVERT: A 666 MET cc_start: 0.8511 (mpp) cc_final: 0.7800 (mpp) REVERT: B 807 LEU cc_start: 0.9478 (tp) cc_final: 0.9249 (mt) REVERT: C 391 TYR cc_start: 0.6608 (m-80) cc_final: 0.6346 (m-80) REVERT: C 405 LYS cc_start: 0.7131 (OUTLIER) cc_final: 0.6866 (ptpt) REVERT: C 459 MET cc_start: 0.4379 (mtm) cc_final: 0.4135 (ttm) REVERT: C 734 LYS cc_start: 0.3797 (tptt) cc_final: 0.3374 (pttm) REVERT: C 761 LYS cc_start: 0.7658 (mmtt) cc_final: 0.7402 (tptt) REVERT: D 499 MET cc_start: -0.0260 (tpp) cc_final: -0.0529 (tpt) REVERT: F 128 HIS cc_start: 0.7704 (m-70) cc_final: 0.7334 (t70) REVERT: F 204 HIS cc_start: 0.6461 (OUTLIER) cc_final: 0.5444 (m170) REVERT: G 56 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8347 (mm-30) REVERT: G 205 GLN cc_start: 0.9246 (tt0) cc_final: 0.8973 (tp40) REVERT: G 208 ARG cc_start: 0.7389 (tmm-80) cc_final: 0.6771 (mtt180) REVERT: H 74 ARG cc_start: 0.9371 (ttp80) cc_final: 0.9134 (mtp-110) REVERT: H 137 SER cc_start: 0.9283 (m) cc_final: 0.9043 (p) REVERT: H 149 ASN cc_start: 0.9041 (t0) cc_final: 0.8688 (t0) outliers start: 40 outliers final: 31 residues processed: 169 average time/residue: 0.3154 time to fit residues: 81.9914 Evaluate side-chains 167 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 134 time to evaluate : 2.187 ------------------------------------------------------------------------------- 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 781 SER 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 B residue 787 ASN Chi-restraints excluded: chain C residue 405 LYS Chi-restraints excluded: chain C residue 486 ASP 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 443 ASP Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 754 VAL Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 158 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 135 ILE Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 204 HIS 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 204 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 206 optimal weight: 1.9990 chunk 24 optimal weight: 20.0000 chunk 121 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 120 optimal weight: 0.9980 chunk 179 optimal weight: 5.9990 chunk 119 optimal weight: 50.0000 chunk 213 optimal weight: 7.9990 chunk 133 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17829 Z= 0.321 Angle : 0.581 9.645 24111 Z= 0.309 Chirality : 0.040 0.176 2738 Planarity : 0.005 0.045 2952 Dihedral : 9.977 88.910 2746 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.17 % Allowed : 16.01 % Favored : 80.82 % 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: 1.03 (0.18), residues: 2211 helix: 1.53 (0.14), residues: 1342 sheet: -1.60 (0.39), residues: 143 loop : -0.32 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 667 HIS 0.003 0.001 HIS H 198 PHE 0.022 0.002 PHE B 542 TYR 0.022 0.001 TYR A 519 ARG 0.005 0.001 ARG C 711 *********************** 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 179 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 139 time to evaluate : 1.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 807 LEU cc_start: 0.9480 (tp) cc_final: 0.9269 (mt) REVERT: C 391 TYR cc_start: 0.6532 (m-80) cc_final: 0.6291 (m-80) REVERT: C 405 LYS cc_start: 0.6987 (OUTLIER) cc_final: 0.6677 (ptpt) REVERT: C 459 MET cc_start: 0.4104 (mtm) cc_final: 0.3858 (ttm) REVERT: C 734 LYS cc_start: 0.3582 (tptt) cc_final: 0.3318 (pttm) REVERT: C 761 LYS cc_start: 0.7698 (mmtt) cc_final: 0.7462 (tptt) REVERT: D 670 MET cc_start: 0.0604 (ptt) cc_final: 0.0088 (ptt) REVERT: F 128 HIS cc_start: 0.7667 (m-70) cc_final: 0.7311 (t70) REVERT: F 204 HIS cc_start: 0.6514 (OUTLIER) cc_final: 0.5486 (m170) REVERT: G 56 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8323 (mm-30) REVERT: G 205 GLN cc_start: 0.9248 (tt0) cc_final: 0.8851 (tp40) REVERT: H 9 GLN cc_start: 0.9271 (mt0) cc_final: 0.8843 (mm110) REVERT: H 74 ARG cc_start: 0.9366 (ttp80) cc_final: 0.9132 (mtp-110) REVERT: H 137 SER cc_start: 0.9295 (m) cc_final: 0.9067 (p) REVERT: H 149 ASN cc_start: 0.9029 (t0) cc_final: 0.8751 (t0) REVERT: H 156 TYR cc_start: 0.9320 (t80) cc_final: 0.9007 (t80) outliers start: 40 outliers final: 34 residues processed: 172 average time/residue: 0.2911 time to fit residues: 78.0976 Evaluate side-chains 168 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 132 time to evaluate : 2.691 ------------------------------------------------------------------------------- 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 781 SER Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 781 SER Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain C residue 405 LYS Chi-restraints excluded: chain C residue 486 ASP 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 443 ASP Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 754 VAL Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 158 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 135 ILE Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 150 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 70 GLU Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain G residue 204 HIS 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 198 HIS Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 131 optimal weight: 0.6980 chunk 85 optimal weight: 30.0000 chunk 127 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 chunk 145 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 chunk 19 optimal weight: 0.5980 chunk 167 optimal weight: 0.7980 chunk 193 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.5086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17829 Z= 0.148 Angle : 0.517 10.921 24111 Z= 0.272 Chirality : 0.038 0.195 2738 Planarity : 0.004 0.045 2952 Dihedral : 8.837 77.848 2746 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.29 % Allowed : 17.18 % Favored : 80.53 % 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: 1.38 (0.18), residues: 2211 helix: 1.77 (0.14), residues: 1344 sheet: -1.37 (0.45), residues: 114 loop : -0.20 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 667 HIS 0.002 0.001 HIS E 204 PHE 0.028 0.001 PHE B 542 TYR 0.019 0.001 TYR B 519 ARG 0.005 0.000 ARG C 711 *********************** 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 185 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 160 time to evaluate : 2.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 MET cc_start: 0.9054 (mmt) cc_final: 0.8627 (mmm) REVERT: B 807 LEU cc_start: 0.9462 (tp) cc_final: 0.9244 (mt) REVERT: C 391 TYR cc_start: 0.6567 (m-80) cc_final: 0.6331 (m-80) REVERT: C 405 LYS cc_start: 0.7097 (OUTLIER) cc_final: 0.6846 (ptpt) REVERT: C 423 GLU cc_start: 0.4906 (OUTLIER) cc_final: 0.4642 (mp0) REVERT: C 459 MET cc_start: 0.4040 (mtm) cc_final: 0.3781 (ttm) REVERT: C 734 LYS cc_start: 0.3652 (tptt) cc_final: 0.3291 (pttm) REVERT: D 616 LEU cc_start: 0.9537 (tp) cc_final: 0.9294 (tp) REVERT: F 128 HIS cc_start: 0.7650 (m-70) cc_final: 0.7323 (t-90) REVERT: F 135 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.8076 (tp) REVERT: F 204 HIS cc_start: 0.5899 (OUTLIER) cc_final: 0.5129 (m170) REVERT: G 56 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8178 (mm-30) REVERT: G 205 GLN cc_start: 0.9269 (tt0) cc_final: 0.8881 (tp40) REVERT: H 9 GLN cc_start: 0.9185 (mt0) cc_final: 0.8842 (mm110) REVERT: H 74 ARG cc_start: 0.9354 (ttp80) cc_final: 0.9151 (mtp-110) REVERT: H 137 SER cc_start: 0.9231 (m) cc_final: 0.9022 (t) REVERT: H 149 ASN cc_start: 0.8964 (t0) cc_final: 0.8489 (t0) REVERT: H 156 TYR cc_start: 0.9135 (t80) cc_final: 0.8872 (t80) outliers start: 25 outliers final: 16 residues processed: 177 average time/residue: 0.2914 time to fit residues: 79.7496 Evaluate side-chains 168 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 148 time to evaluate : 2.063 ------------------------------------------------------------------------------- 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 B residue 787 ASN Chi-restraints excluded: chain C residue 405 LYS 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 E residue 198 HIS Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 150 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 134 VAL 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: 10.0000 chunk 186 optimal weight: 6.9990 chunk 198 optimal weight: 2.9990 chunk 119 optimal weight: 30.0000 chunk 86 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 179 optimal weight: 3.9990 chunk 187 optimal weight: 9.9990 chunk 197 optimal weight: 10.0000 chunk 130 optimal weight: 0.8980 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.5312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 17829 Z= 0.387 Angle : 0.640 11.406 24111 Z= 0.337 Chirality : 0.041 0.220 2738 Planarity : 0.005 0.045 2952 Dihedral : 9.678 86.594 2746 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.82 % Allowed : 16.89 % Favored : 80.29 % 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: 1.11 (0.18), residues: 2211 helix: 1.55 (0.14), residues: 1342 sheet: -1.52 (0.40), residues: 144 loop : -0.19 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 667 HIS 0.004 0.001 HIS H 198 PHE 0.026 0.002 PHE B 542 TYR 0.024 0.002 TYR A 519 ARG 0.006 0.001 ARG A 481 *********************** 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 166 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 132 time to evaluate : 2.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 520 GLU cc_start: 0.8720 (mp0) cc_final: 0.8365 (mm-30) REVERT: C 391 TYR cc_start: 0.6375 (m-80) cc_final: 0.6144 (m-80) REVERT: C 405 LYS cc_start: 0.6991 (OUTLIER) cc_final: 0.6628 (ptpt) REVERT: C 423 GLU cc_start: 0.4974 (OUTLIER) cc_final: 0.4643 (mp0) REVERT: C 459 MET cc_start: 0.4437 (mtm) cc_final: 0.4222 (ttm) REVERT: C 686 MET cc_start: 0.0055 (tpt) cc_final: -0.0668 (mmp) REVERT: C 734 LYS cc_start: 0.3682 (tptt) cc_final: 0.3295 (pttm) REVERT: C 761 LYS cc_start: 0.7796 (tptt) cc_final: 0.7414 (mttp) REVERT: D 666 MET cc_start: 0.2605 (tpp) cc_final: 0.2335 (tpt) REVERT: F 128 HIS cc_start: 0.7645 (m-70) cc_final: 0.7349 (t-90) REVERT: F 204 HIS cc_start: 0.6282 (OUTLIER) cc_final: 0.5265 (m170) REVERT: G 56 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8350 (mt-10) REVERT: G 205 GLN cc_start: 0.9265 (tt0) cc_final: 0.8879 (tp40) REVERT: H 149 ASN cc_start: 0.8924 (t0) cc_final: 0.8667 (m-40) REVERT: H 156 TYR cc_start: 0.9351 (t80) cc_final: 0.9051 (t80) outliers start: 34 outliers final: 28 residues processed: 158 average time/residue: 0.3086 time to fit residues: 77.6841 Evaluate side-chains 157 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 126 time to evaluate : 2.004 ------------------------------------------------------------------------------- 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 781 SER Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 781 SER Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain C residue 405 LYS 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 748 LYS Chi-restraints excluded: chain D residue 443 ASP Chi-restraints excluded: chain D residue 717 MET Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 150 ILE 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 135 ILE Chi-restraints excluded: chain F residue 150 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 G residue 204 HIS Chi-restraints excluded: chain H residue 134 VAL 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: 7.9990 chunk 128 optimal weight: 0.7980 chunk 99 optimal weight: 9.9990 chunk 145 optimal weight: 0.5980 chunk 220 optimal weight: 1.9990 chunk 202 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.5354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 17829 Z= 0.198 Angle : 0.580 10.628 24111 Z= 0.302 Chirality : 0.039 0.197 2738 Planarity : 0.004 0.045 2952 Dihedral : 9.326 89.316 2746 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.29 % Allowed : 17.71 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.27 (0.18), residues: 2211 helix: 1.68 (0.14), residues: 1342 sheet: -1.61 (0.37), residues: 160 loop : -0.06 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 667 HIS 0.004 0.001 HIS F 60 PHE 0.031 0.001 PHE B 542 TYR 0.018 0.001 TYR B 519 ARG 0.007 0.000 ARG H 74 ********************** 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 167 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 142 time to evaluate : 2.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 807 LEU cc_start: 0.9474 (tp) cc_final: 0.9259 (mt) REVERT: C 391 TYR cc_start: 0.6696 (m-80) cc_final: 0.6476 (m-80) REVERT: C 405 LYS cc_start: 0.7280 (OUTLIER) cc_final: 0.7050 (ptpt) REVERT: C 423 GLU cc_start: 0.4963 (OUTLIER) cc_final: 0.4638 (mp0) REVERT: C 459 MET cc_start: 0.4387 (mtm) cc_final: 0.4166 (ttm) REVERT: C 686 MET cc_start: 0.0005 (tpt) cc_final: -0.0565 (mmp) REVERT: C 717 MET cc_start: 0.6955 (pmm) cc_final: 0.6669 (pmm) REVERT: C 734 LYS cc_start: 0.3736 (tptt) cc_final: 0.3365 (pttm) REVERT: C 761 LYS cc_start: 0.7774 (tptt) cc_final: 0.7384 (mttp) REVERT: F 128 HIS cc_start: 0.7654 (m-70) cc_final: 0.7365 (t-90) REVERT: F 204 HIS cc_start: 0.6146 (OUTLIER) cc_final: 0.5163 (m170) REVERT: G 56 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8302 (mt-10) REVERT: G 205 GLN cc_start: 0.9261 (tt0) cc_final: 0.8871 (tp40) REVERT: H 156 TYR cc_start: 0.9240 (t80) cc_final: 0.8951 (t80) outliers start: 25 outliers final: 22 residues processed: 160 average time/residue: 0.2800 time to fit residues: 70.5033 Evaluate side-chains 163 residues out of total 1853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 138 time to evaluate : 2.101 ------------------------------------------------------------------------------- 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 781 SER 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 B residue 787 ASN Chi-restraints excluded: chain C residue 405 LYS 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 748 LYS Chi-restraints excluded: chain D residue 717 MET Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 134 VAL 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: 4.9990 chunk 53 optimal weight: 0.3980 chunk 161 optimal weight: 0.7980 chunk 25 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 180 optimal weight: 20.0000 chunk 22 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 154 optimal weight: 7.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 160 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 = 0.4161 r_free = 0.4161 target = 0.123060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.077154 restraints weight = 161267.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.078857 restraints weight = 50981.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.078291 restraints weight = 32361.115| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.5470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 17829 Z= 0.313 Angle : 0.607 10.289 24111 Z= 0.319 Chirality : 0.040 0.199 2738 Planarity : 0.005 0.045 2952 Dihedral : 9.520 81.944 2746 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.64 % Allowed : 17.42 % Favored : 79.94 % 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: 1.28 (0.18), residues: 2211 helix: 1.67 (0.14), residues: 1327 sheet: -1.58 (0.38), residues: 158 loop : 0.01 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP D 667 HIS 0.004 0.001 HIS G 60 PHE 0.028 0.002 PHE B 542 TYR 0.022 0.001 TYR A 519 ARG 0.008 0.001 ARG H 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3195.45 seconds wall clock time: 60 minutes 6.91 seconds (3606.91 seconds total)