Starting phenix.real_space_refine on Fri Feb 16 17:35:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aym_15716/02_2024/8aym_15716_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aym_15716/02_2024/8aym_15716.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aym_15716/02_2024/8aym_15716.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aym_15716/02_2024/8aym_15716.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aym_15716/02_2024/8aym_15716_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aym_15716/02_2024/8aym_15716_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 7 Type Number sf(0) Gaussians P 10 5.49 5 S 92 5.16 5 Cl 2 4.86 5 C 10462 2.51 5 N 2506 2.21 5 O 2872 1.98 5 F 18 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 216": "OE1" <-> "OE2" Residue "I GLU 232": "OE1" <-> "OE2" Residue "C TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 415": "OD1" <-> "OD2" Residue "C TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 418": "OE1" <-> "OE2" Residue "C GLU 423": "OE1" <-> "OE2" Residue "C TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 439": "OE1" <-> "OE2" Residue "C ASP 443": "OD1" <-> "OD2" Residue "C GLU 462": "OE1" <-> "OE2" Residue "C TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 482": "OE1" <-> "OE2" Residue "C GLU 483": "OE1" <-> "OE2" Residue "C GLU 546": "OE1" <-> "OE2" Residue "C PHE 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 630": "OE1" <-> "OE2" Residue "C TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 683": "OE1" <-> "OE2" Residue "C TYR 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 751": "OE1" <-> "OE2" Residue "C PHE 792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 809": "OE1" <-> "OE2" Residue "C TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 422": "OE1" <-> "OE2" Residue "D PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 456": "OD1" <-> "OD2" Residue "D TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 590": "OD1" <-> "OD2" Residue "D PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 657": "OE1" <-> "OE2" Residue "D ASP 668": "OD1" <-> "OD2" Residue "D GLU 678": "OE1" <-> "OE2" Residue "D PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 713": "OE1" <-> "OE2" Residue "D ASP 719": "OD1" <-> "OD2" Residue "D ASP 728": "OD1" <-> "OD2" Residue "D TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 769": "OD1" <-> "OD2" Residue "D GLU 772": "OE1" <-> "OE2" Residue "D ASP 777": "OD1" <-> "OD2" Residue "D PHE 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 813": "OE1" <-> "OE2" Residue "D TYR 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 422": "OE1" <-> "OE2" Residue "B PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 456": "OD1" <-> "OD2" Residue "B TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 590": "OD1" <-> "OD2" Residue "B PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 657": "OE1" <-> "OE2" Residue "B ASP 668": "OD1" <-> "OD2" Residue "B GLU 678": "OE1" <-> "OE2" Residue "B PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 713": "OE1" <-> "OE2" Residue "B ASP 719": "OD1" <-> "OD2" Residue "B ASP 728": "OD1" <-> "OD2" Residue "B TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 755": "OE1" <-> "OE2" Residue "B ASP 769": "OD1" <-> "OD2" Residue "B GLU 772": "OE1" <-> "OE2" Residue "B ASP 777": "OD1" <-> "OD2" Residue "B PHE 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 813": "OE1" <-> "OE2" Residue "B TYR 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 415": "OD1" <-> "OD2" Residue "A TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 418": "OE1" <-> "OE2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A GLU 439": "OE1" <-> "OE2" Residue "A ASP 443": "OD1" <-> "OD2" Residue "A GLU 462": "OE1" <-> "OE2" Residue "A TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 482": "OE1" <-> "OE2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "A ASP 486": "OD1" <-> "OD2" Residue "A GLU 546": "OE1" <-> "OE2" Residue "A PHE 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 630": "OE1" <-> "OE2" Residue "A TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 683": "OE1" <-> "OE2" Residue "A TYR 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 751": "OE1" <-> "OE2" Residue "A PHE 792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 809": "OE1" <-> "OE2" Residue "A TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 216": "OE1" <-> "OE2" Residue "J GLU 232": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15962 Number of models: 1 Model: "" Number of chains: 12 Chain: "I" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1358 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 2, 'TRANS': 182} Chain breaks: 2 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 47 Chain: "C" Number of atoms: 3168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3168 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 399} Chain breaks: 1 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 81 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "D" Number of atoms: 3103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3103 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 3103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3103 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "A" Number of atoms: 3168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3168 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 399} Chain breaks: 1 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 81 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "J" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1358 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 2, 'TRANS': 182} Chain breaks: 2 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 47 Chain: "I" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'PLM': 1, 'XVD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 186 Unusual residues: {'PLM': 4, 'POV': 2, 'ZK1': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "D" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 126 Unusual residues: {'OLC': 1, 'PLM': 2, 'POV': 1, 'ZK1': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 126 Unusual residues: {'OLC': 1, 'PLM': 2, 'POV': 1, 'ZK1': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "A" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 186 Unusual residues: {'PLM': 4, 'POV': 2, 'ZK1': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "J" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'PLM': 1, 'XVD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.53, per 1000 atoms: 0.60 Number of scatterers: 15962 At special positions: 0 Unit cell: (131.61, 110.21, 132.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 2 17.00 S 92 16.00 P 10 15.00 F 18 9.00 O 2872 8.00 N 2506 7.00 C 10462 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS I 52 " - pdb=" SG CYS I 91 " distance=2.03 Simple disulfide: pdb=" SG CYS I 90 " - pdb=" SG CYS I 100 " distance=2.03 Simple disulfide: pdb=" SG CYS C 714 " - pdb=" SG CYS C 769 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS A 714 " - pdb=" SG CYS A 769 " distance=2.03 Simple disulfide: pdb=" SG CYS J 52 " - pdb=" SG CYS J 91 " distance=2.03 Simple disulfide: pdb=" SG CYS J 90 " - pdb=" SG CYS J 100 " 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: 6.84 Conformation dependent library (CDL) restraints added in 3.2 seconds 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3656 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 74 helices and 16 sheets defined 49.6% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.60 Creating SS restraints... Processing helix chain 'I' and resid 20 through 39 Processing helix chain 'I' and resid 116 through 127 Processing helix chain 'I' and resid 129 through 149 Processing helix chain 'I' and resid 156 through 183 removed outlier: 3.573A pdb=" N GLY I 169 " --> pdb=" O PHE I 165 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR I 179 " --> pdb=" O GLY I 175 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 232 Processing helix chain 'C' and resid 413 through 416 Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 458 through 464 Processing helix chain 'C' and resid 479 through 484 removed outlier: 3.850A pdb=" N VAL C 484 " --> pdb=" O VAL C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 540 Processing helix chain 'C' and resid 544 through 547 No H-bonds generated for 'chain 'C' and resid 544 through 547' Processing helix chain 'C' and resid 569 through 580 Processing helix chain 'C' and resid 592 through 624 Processing helix chain 'C' and resid 632 through 637 Processing helix chain 'C' and resid 650 through 657 removed outlier: 3.780A pdb=" N ARG C 657 " --> pdb=" O GLU C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 661 through 672 removed outlier: 3.560A pdb=" N LYS C 671 " --> pdb=" O TRP C 667 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER C 672 " --> pdb=" O THR C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 691 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 789 through 814 Processing helix chain 'D' and resid 417 through 420 Processing helix chain 'D' and resid 424 through 436 removed outlier: 3.861A pdb=" N ALA D 430 " --> pdb=" O VAL D 426 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 468 removed outlier: 3.647A pdb=" N LEU D 467 " --> pdb=" O MET D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 486 No H-bonds generated for 'chain 'D' and resid 483 through 486' Processing helix chain 'D' and resid 523 through 546 Processing helix chain 'D' and resid 573 through 584 Processing helix chain 'D' and resid 596 through 625 Processing helix chain 'D' and resid 637 through 641 Processing helix chain 'D' and resid 654 through 661 Processing helix chain 'D' and resid 665 through 675 removed outlier: 3.583A pdb=" N TYR D 673 " --> pdb=" O LYS D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 696 Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 742 through 756 removed outlier: 4.325A pdb=" N LEU D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS D 752 " --> pdb=" O LEU D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 767 Processing helix chain 'D' and resid 777 through 779 No H-bonds generated for 'chain 'D' and resid 777 through 779' Processing helix chain 'D' and resid 793 through 818 Processing helix chain 'B' and resid 417 through 420 Processing helix chain 'B' and resid 424 through 436 removed outlier: 3.862A pdb=" N ALA B 430 " --> pdb=" O VAL B 426 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 468 removed outlier: 3.638A pdb=" N LEU B 467 " --> pdb=" O MET B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 486 No H-bonds generated for 'chain 'B' and resid 483 through 486' Processing helix chain 'B' and resid 523 through 546 Processing helix chain 'B' and resid 573 through 584 Processing helix chain 'B' and resid 596 through 625 Processing helix chain 'B' and resid 637 through 641 Processing helix chain 'B' and resid 654 through 661 Processing helix chain 'B' and resid 665 through 675 removed outlier: 3.585A pdb=" N TYR B 673 " --> pdb=" O LYS B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 696 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 742 through 756 removed outlier: 4.307A pdb=" N LEU B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS B 752 " --> pdb=" O LEU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 767 Processing helix chain 'B' and resid 777 through 779 No H-bonds generated for 'chain 'B' and resid 777 through 779' Processing helix chain 'B' and resid 793 through 818 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 464 Processing helix chain 'A' and resid 479 through 484 removed outlier: 3.848A pdb=" N VAL A 484 " --> pdb=" O VAL A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 540 Processing helix chain 'A' and resid 544 through 547 No H-bonds generated for 'chain 'A' and resid 544 through 547' Processing helix chain 'A' and resid 569 through 580 Processing helix chain 'A' and resid 592 through 624 Processing helix chain 'A' and resid 632 through 637 Processing helix chain 'A' and resid 650 through 657 removed outlier: 3.781A pdb=" N ARG A 657 " --> pdb=" O GLU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 672 removed outlier: 3.559A pdb=" N LYS A 671 " --> pdb=" O TRP A 667 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 672 " --> pdb=" O THR A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 691 Processing helix chain 'A' and resid 702 through 710 Processing helix chain 'A' and resid 739 through 751 Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 789 through 814 Processing helix chain 'J' and resid 20 through 39 Processing helix chain 'J' and resid 116 through 127 Processing helix chain 'J' and resid 129 through 149 Processing helix chain 'J' and resid 156 through 183 removed outlier: 3.573A pdb=" N GLY J 169 " --> pdb=" O PHE J 165 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR J 179 " --> pdb=" O GLY J 175 " (cutoff:3.500A) Processing helix chain 'J' and resid 203 through 232 Processing sheet with id= A, first strand: chain 'I' and resid 88 through 90 Processing sheet with id= B, first strand: chain 'C' and resid 447 through 450 removed outlier: 3.885A pdb=" N ALA C 448 " --> pdb=" O ASN C 457 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 485 through 487 Processing sheet with id= D, first strand: chain 'C' and resid 492 through 494 removed outlier: 3.897A pdb=" N MET C 492 " --> pdb=" O TYR C 728 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 716 through 719 removed outlier: 3.822A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LYS C 501 " --> pdb=" O TYR C 696 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N TYR C 696 " --> pdb=" O LYS C 501 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 9.302A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 489 through 491 Processing sheet with id= G, first strand: chain 'D' and resid 720 through 723 removed outlier: 3.985A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.095A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 494 through 498 removed outlier: 7.021A pdb=" N TYR D 732 " --> pdb=" O PHE D 495 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N SER D 497 " --> pdb=" O LYS D 730 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LYS D 730 " --> pdb=" O SER D 497 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 489 through 491 Processing sheet with id= J, first strand: chain 'B' and resid 720 through 723 removed outlier: 3.984A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.094A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 494 through 498 removed outlier: 7.042A pdb=" N TYR B 732 " --> pdb=" O PHE B 495 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N SER B 497 " --> pdb=" O LYS B 730 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LYS B 730 " --> pdb=" O SER B 497 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 447 through 450 removed outlier: 3.874A pdb=" N ALA A 448 " --> pdb=" O ASN A 457 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 485 through 487 Processing sheet with id= N, first strand: chain 'A' and resid 492 through 494 removed outlier: 3.900A pdb=" N MET A 492 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 716 through 719 removed outlier: 3.820A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LYS A 501 " --> pdb=" O TYR A 696 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N TYR A 696 " --> pdb=" O LYS A 501 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA A 642 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N LEU A 699 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLY A 644 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 9.304A pdb=" N GLU A 701 " --> pdb=" O GLY A 644 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'J' and resid 88 through 90 736 hydrogen bonds defined for protein. 2184 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: 4.31 Time building geometry restraints manager: 7.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2468 1.32 - 1.45: 4634 1.45 - 1.59: 9014 1.59 - 1.72: 12 1.72 - 1.86: 154 Bond restraints: 16282 Sorted by residual: bond pdb=" CAW ZK1 B 901 " pdb=" NAY ZK1 B 901 " ideal model delta sigma weight residual 1.388 1.505 -0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" CAW ZK1 D 901 " pdb=" NAY ZK1 D 901 " ideal model delta sigma weight residual 1.388 1.503 -0.115 2.00e-02 2.50e+03 3.32e+01 bond pdb=" CAW ZK1 C 901 " pdb=" NAY ZK1 C 901 " ideal model delta sigma weight residual 1.388 1.499 -0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" CAW ZK1 A 901 " pdb=" NAY ZK1 A 901 " ideal model delta sigma weight residual 1.388 1.498 -0.110 2.00e-02 2.50e+03 3.02e+01 bond pdb=" CAV ZK1 B 901 " pdb=" NAP ZK1 B 901 " ideal model delta sigma weight residual 1.381 1.485 -0.104 2.00e-02 2.50e+03 2.69e+01 ... (remaining 16277 not shown) Histogram of bond angle deviations from ideal: 97.85 - 106.85: 342 106.85 - 115.84: 10203 115.84 - 124.84: 11074 124.84 - 133.84: 269 133.84 - 142.83: 56 Bond angle restraints: 21944 Sorted by residual: angle pdb=" C35 POV A 905 " pdb=" C36 POV A 905 " pdb=" C37 POV A 905 " ideal model delta sigma weight residual 113.93 142.83 -28.90 3.00e+00 1.11e-01 9.28e+01 angle pdb=" C35 POV C 905 " pdb=" C36 POV C 905 " pdb=" C37 POV C 905 " ideal model delta sigma weight residual 113.93 142.82 -28.89 3.00e+00 1.11e-01 9.27e+01 angle pdb=" C35 POV A 902 " pdb=" C36 POV A 902 " pdb=" C37 POV A 902 " ideal model delta sigma weight residual 113.93 142.04 -28.11 3.00e+00 1.11e-01 8.78e+01 angle pdb=" C35 POV C 902 " pdb=" C36 POV C 902 " pdb=" C37 POV C 902 " ideal model delta sigma weight residual 113.93 142.00 -28.07 3.00e+00 1.11e-01 8.76e+01 angle pdb=" C35 POV D 905 " pdb=" C36 POV D 905 " pdb=" C37 POV D 905 " ideal model delta sigma weight residual 113.93 141.82 -27.89 3.00e+00 1.11e-01 8.64e+01 ... (remaining 21939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.04: 9048 26.04 - 52.07: 502 52.07 - 78.11: 99 78.11 - 104.15: 27 104.15 - 130.18: 6 Dihedral angle restraints: 9682 sinusoidal: 3936 harmonic: 5746 Sorted by residual: dihedral pdb=" C27 POV B 905 " pdb=" C28 POV B 905 " pdb=" C29 POV B 905 " pdb="C210 POV B 905 " ideal model delta sinusoidal sigma weight residual 127.48 -102.34 -130.18 1 3.00e+01 1.11e-03 1.75e+01 dihedral pdb=" C27 POV D 905 " pdb=" C28 POV D 905 " pdb=" C29 POV D 905 " pdb="C210 POV D 905 " ideal model delta sinusoidal sigma weight residual 127.48 -102.37 -130.15 1 3.00e+01 1.11e-03 1.75e+01 dihedral pdb=" CA SER D 497 " pdb=" C SER D 497 " pdb=" N LEU D 498 " pdb=" CA LEU D 498 " ideal model delta harmonic sigma weight residual 180.00 -159.39 -20.61 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 9679 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1761 0.044 - 0.088: 529 0.088 - 0.132: 108 0.132 - 0.176: 12 0.176 - 0.221: 6 Chirality restraints: 2416 Sorted by residual: chirality pdb=" CB VAL C 600 " pdb=" CA VAL C 600 " pdb=" CG1 VAL C 600 " pdb=" CG2 VAL C 600 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CB VAL A 600 " pdb=" CA VAL A 600 " pdb=" CG1 VAL A 600 " pdb=" CG2 VAL A 600 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C22 OLC D 902 " pdb=" C21 OLC D 902 " pdb=" C24 OLC D 902 " pdb=" O23 OLC D 902 " both_signs ideal model delta sigma weight residual False -2.31 -2.50 0.19 2.00e-01 2.50e+01 9.10e-01 ... (remaining 2413 not shown) Planarity restraints: 2658 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 744 " -0.037 5.00e-02 4.00e+02 5.66e-02 5.13e+00 pdb=" N PRO B 745 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 745 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 745 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 744 " 0.038 5.00e-02 4.00e+02 5.66e-02 5.13e+00 pdb=" N PRO D 745 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO D 745 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 745 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 519 " 0.030 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO D 520 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO D 520 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 520 " 0.025 5.00e-02 4.00e+02 ... (remaining 2655 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 204 2.64 - 3.20: 14850 3.20 - 3.77: 23447 3.77 - 4.33: 33666 4.33 - 4.90: 56112 Nonbonded interactions: 128279 Sorted by model distance: nonbonded pdb=" O ILE J 37 " pdb=" OG1 THR J 41 " model vdw 2.075 2.440 nonbonded pdb=" O ILE I 37 " pdb=" OG1 THR I 41 " model vdw 2.075 2.440 nonbonded pdb=" O VAL C 677 " pdb=" OH TYR C 696 " model vdw 2.209 2.440 nonbonded pdb=" O VAL A 677 " pdb=" OH TYR A 696 " model vdw 2.209 2.440 nonbonded pdb=" N ALA A 448 " pdb=" OD1 ASN A 457 " model vdw 2.231 2.520 ... (remaining 128274 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 393 through 398 or resid 400 through 403 or resid 405 thro \ ugh 407 or resid 412 through 414 or resid 416 through 422 or resid 424 through 4 \ 31 or resid 433 or resid 436 or (resid 438 and (name N or name CA or name C or n \ ame O or name CB )) or resid 440 through 441 or resid 443 through 450 or resid 4 \ 52 through 454 or resid 456 through 466 or resid 468 through 469 or resid 471 or \ resid 473 through 544 or (resid 545 through 546 and (name N or name CA or name \ C or name O or name CB )) or resid 567 through 581 or resid 583 through 635 or r \ esid 637 through 638 or (resid 639 through 640 and (name N or name CA or name C \ or name O or name CB )) or resid 641 through 646 or resid 649 through 663 or res \ id 665 through 670 or resid 672 through 679 or (resid 680 and (name N or name CA \ or name C or name O or name CB )) or resid 681 through 682 or resid 684 through \ 685 or resid 688 through 736 or resid 738 or resid 741 through 759 or (resid 76 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 762 through \ 770 or resid 772 through 777 or resid 779 through 795 or resid 797 through 815 o \ r resid 901 or resid 903 through 904 or (resid 905 and (name N or name C1 or nam \ e C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name O11 or name O12 or name O13 or name O14 or n \ ame O21 or name O22 or name O31 or name O32 or name P or name C210 or name C211 \ or name C212 or name C213)))) selection = (chain 'B' and (resid 397 through 402 or resid 404 through 407 or resid 409 or ( \ resid 410 and (name N or name CA or name C or name O or name CB )) or resid 411 \ or resid 416 through 418 or resid 420 through 426 or resid 428 through 435 or re \ sid 437 or resid 440 or resid 442 or resid 444 through 445 or resid 447 through \ 453 or (resid 454 and (name N or name CA or name C or name O or name CB )) or (r \ esid 456 and (name N or name CA or name C or name O or name CB )) or resid 457 o \ r (resid 458 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 60 through 470 or resid 472 through 473 or resid 475 or resid 477 through 507 or \ (resid 508 through 509 and (name N or name CA or name C or name O or name CB )) \ or resid 510 through 585 or resid 587 through 639 or resid 641 through 650 or r \ esid 653 through 656 or (resid 657 and (name N or name CA or name C or name O or \ name CB )) or resid 658 through 667 or resid 669 through 674 or resid 676 throu \ gh 686 or resid 688 through 689 or resid 692 through 696 or (resid 697 and (name \ N or name CA or name C or name O or name CB )) or resid 698 through 718 or (res \ id 719 and (name N or name CA or name C or name O or name CB )) or resid 720 thr \ ough 740 or resid 742 or resid 745 through 763 or resid 765 through 774 or (resi \ d 776 through 778 and (name N or name CA or name C or name O or name CB )) or re \ sid 779 or (resid 780 through 781 and (name N or name CA or name C or name O or \ name CB )) or (resid 783 and (name N or name CA or name C or name O or name CB ) \ ) or resid 784 through 799 or resid 801 through 817 or (resid 818 through 819 an \ d (name N or name CA or name C or name O or name CB )) or resid 901 or (resid 90 \ 3 and (name CA or name CB or name CD or name CE or name C1 or name C2 or name C3 \ or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name CC or \ name O1 or name O2 )) or resid 904 through 905)) selection = (chain 'C' and (resid 393 through 398 or resid 400 through 403 or resid 405 thro \ ugh 407 or resid 412 through 414 or resid 416 through 422 or resid 424 through 4 \ 31 or resid 433 or resid 436 or (resid 438 and (name N or name CA or name C or n \ ame O or name CB )) or resid 440 through 441 or resid 443 through 450 or resid 4 \ 52 through 454 or resid 456 through 466 or resid 468 through 469 or resid 471 or \ resid 473 through 544 or (resid 545 through 546 and (name N or name CA or name \ C or name O or name CB )) or resid 567 through 581 or resid 583 through 635 or r \ esid 637 through 638 or (resid 639 through 640 and (name N or name CA or name C \ or name O or name CB )) or resid 641 through 646 or resid 649 through 663 or res \ id 665 through 670 or resid 672 through 679 or (resid 680 and (name N or name CA \ or name C or name O or name CB )) or resid 681 through 682 or resid 684 through \ 685 or resid 688 through 736 or resid 738 or resid 741 through 759 or (resid 76 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 762 through \ 770 or resid 772 through 777 or resid 779 through 795 or resid 797 through 815 o \ r resid 901 or resid 903 through 904 or (resid 905 and (name N or name C1 or nam \ e C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name O11 or name O12 or name O13 or name O14 or n \ ame O21 or name O22 or name O31 or name O32 or name P or name C210 or name C211 \ or name C212 or name C213)))) selection = (chain 'D' and (resid 397 through 402 or resid 404 through 407 or resid 409 or ( \ resid 410 and (name N or name CA or name C or name O or name CB )) or resid 411 \ or resid 416 through 418 or resid 420 through 426 or resid 428 through 435 or re \ sid 437 or resid 440 or resid 442 or resid 444 through 445 or resid 447 through \ 453 or (resid 454 and (name N or name CA or name C or name O or name CB )) or (r \ esid 456 and (name N or name CA or name C or name O or name CB )) or resid 457 o \ r (resid 458 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 60 through 470 or resid 472 through 473 or resid 475 or resid 477 through 507 or \ (resid 508 through 509 and (name N or name CA or name C or name O or name CB )) \ or resid 510 through 585 or resid 587 through 639 or resid 641 through 650 or r \ esid 653 through 656 or (resid 657 and (name N or name CA or name C or name O or \ name CB )) or resid 658 through 667 or resid 669 through 674 or resid 676 throu \ gh 686 or resid 688 through 689 or resid 692 through 696 or (resid 697 and (name \ N or name CA or name C or name O or name CB )) or resid 698 through 718 or (res \ id 719 and (name N or name CA or name C or name O or name CB )) or resid 720 thr \ ough 740 or resid 742 or resid 745 through 763 or resid 765 through 774 or (resi \ d 776 through 778 and (name N or name CA or name C or name O or name CB )) or re \ sid 779 or (resid 780 through 781 and (name N or name CA or name C or name O or \ name CB )) or (resid 783 and (name N or name CA or name C or name O or name CB ) \ ) or resid 784 through 799 or resid 801 through 817 or (resid 818 through 819 an \ d (name N or name CA or name C or name O or name CB )) or resid 901 or (resid 90 \ 3 and (name CA or name CB or name CD or name CE or name C1 or name C2 or name C3 \ or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name CC or \ name O1 or name O2 )) or resid 904 through 905)) } ncs_group { reference = (chain 'I' and resid 16 through 234) selection = (chain 'J' and resid 16 through 234) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.300 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: 7.430 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 46.580 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 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 : 0.008 0.117 16282 Z= 0.528 Angle : 1.270 28.901 21944 Z= 0.508 Chirality : 0.043 0.221 2416 Planarity : 0.004 0.057 2658 Dihedral : 17.620 130.182 6002 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.13 % Allowed : 0.13 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.18), residues: 1980 helix: 0.28 (0.16), residues: 1080 sheet: -2.66 (0.41), residues: 138 loop : -1.10 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 460 HIS 0.010 0.002 HIS A 548 PHE 0.024 0.002 PHE B 541 TYR 0.031 0.002 TYR B 816 ARG 0.024 0.001 ARG C 624 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 270 time to evaluate : 1.731 Fit side-chains REVERT: C 421 CYS cc_start: 0.8024 (m) cc_final: 0.7784 (m) REVERT: C 638 GLN cc_start: 0.8017 (pp30) cc_final: 0.7607 (pp30) REVERT: A 421 CYS cc_start: 0.8065 (m) cc_final: 0.7716 (m) REVERT: A 638 GLN cc_start: 0.7962 (pp30) cc_final: 0.7549 (pp30) outliers start: 2 outliers final: 0 residues processed: 272 average time/residue: 0.3142 time to fit residues: 122.1158 Evaluate side-chains 180 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 3.9990 chunk 150 optimal weight: 0.0040 chunk 83 optimal weight: 1.9990 chunk 51 optimal weight: 0.0570 chunk 101 optimal weight: 0.5980 chunk 80 optimal weight: 0.0060 chunk 155 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 94 optimal weight: 0.8980 chunk 115 optimal weight: 0.5980 chunk 179 optimal weight: 0.6980 overall best weight: 0.2526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 431 HIS D 726 ASN B 726 ASN A 431 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16282 Z= 0.147 Angle : 0.503 12.275 21944 Z= 0.254 Chirality : 0.039 0.199 2416 Planarity : 0.004 0.055 2658 Dihedral : 13.808 140.336 2702 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.40 % Allowed : 7.91 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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: 0.46 (0.19), residues: 1980 helix: 1.61 (0.16), residues: 1088 sheet: -2.44 (0.41), residues: 134 loop : -1.09 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 766 HIS 0.006 0.001 HIS A 548 PHE 0.019 0.001 PHE A 810 TYR 0.016 0.001 TYR B 673 ARG 0.004 0.000 ARG A 416 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 202 time to evaluate : 1.665 Fit side-chains revert: symmetry clash REVERT: C 421 CYS cc_start: 0.8072 (m) cc_final: 0.7672 (m) REVERT: C 638 GLN cc_start: 0.8028 (pp30) cc_final: 0.7733 (pp30) REVERT: D 434 LYS cc_start: 0.7432 (tmmt) cc_final: 0.7222 (ttmt) REVERT: D 714 GLN cc_start: 0.7222 (OUTLIER) cc_final: 0.6928 (tp40) REVERT: B 434 LYS cc_start: 0.7411 (tmmt) cc_final: 0.7172 (ttmt) REVERT: A 421 CYS cc_start: 0.8034 (m) cc_final: 0.7653 (m) REVERT: A 638 GLN cc_start: 0.7982 (pp30) cc_final: 0.7682 (pp30) outliers start: 22 outliers final: 11 residues processed: 214 average time/residue: 0.2832 time to fit residues: 89.7355 Evaluate side-chains 177 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 165 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 714 GLN Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 755 GLU Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 719 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 2.9990 chunk 55 optimal weight: 0.0070 chunk 149 optimal weight: 1.9990 chunk 122 optimal weight: 0.3980 chunk 49 optimal weight: 2.9990 chunk 180 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 160 optimal weight: 0.9990 chunk 178 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 overall best weight: 0.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 431 HIS C 710 GLN B 619 ASN A 431 HIS A 710 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16282 Z= 0.224 Angle : 0.525 13.225 21944 Z= 0.264 Chirality : 0.041 0.249 2416 Planarity : 0.004 0.058 2658 Dihedral : 13.315 139.055 2702 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.91 % Allowed : 10.52 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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: 0.76 (0.19), residues: 1980 helix: 1.92 (0.16), residues: 1086 sheet: -2.08 (0.40), residues: 144 loop : -1.08 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 766 HIS 0.004 0.001 HIS J 83 PHE 0.014 0.002 PHE C 491 TYR 0.014 0.002 TYR C 519 ARG 0.003 0.000 ARG B 485 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 193 time to evaluate : 1.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 421 CYS cc_start: 0.8028 (m) cc_final: 0.7509 (m) REVERT: C 436 TYR cc_start: 0.8201 (p90) cc_final: 0.7627 (p90) REVERT: C 638 GLN cc_start: 0.8364 (pp30) cc_final: 0.7716 (pp30) REVERT: D 523 TYR cc_start: 0.7909 (m-10) cc_final: 0.7635 (m-10) REVERT: B 523 TYR cc_start: 0.7873 (m-10) cc_final: 0.7591 (m-10) REVERT: B 674 MET cc_start: 0.7276 (mmm) cc_final: 0.7042 (mmm) REVERT: A 421 CYS cc_start: 0.8034 (m) cc_final: 0.7507 (m) REVERT: A 436 TYR cc_start: 0.8173 (p90) cc_final: 0.7510 (p90) REVERT: A 638 GLN cc_start: 0.8371 (pp30) cc_final: 0.7721 (pp30) outliers start: 30 outliers final: 23 residues processed: 212 average time/residue: 0.2947 time to fit residues: 92.6148 Evaluate side-chains 179 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 156 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain B residue 755 GLU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain J residue 150 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 0.8980 chunk 135 optimal weight: 8.9990 chunk 93 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 180 optimal weight: 5.9990 chunk 191 optimal weight: 0.9990 chunk 94 optimal weight: 0.0030 chunk 171 optimal weight: 2.9990 chunk 51 optimal weight: 0.0030 overall best weight: 0.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 710 GLN ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 726 ASN B 726 ASN A 431 HIS A 710 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16282 Z= 0.150 Angle : 0.456 13.042 21944 Z= 0.229 Chirality : 0.038 0.234 2416 Planarity : 0.004 0.057 2658 Dihedral : 12.576 123.595 2702 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.53 % Allowed : 11.35 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.20), residues: 1980 helix: 2.18 (0.16), residues: 1084 sheet: -1.95 (0.38), residues: 162 loop : -0.95 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 766 HIS 0.004 0.001 HIS A 548 PHE 0.010 0.001 PHE A 810 TYR 0.012 0.001 TYR D 424 ARG 0.001 0.000 ARG J 122 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 176 time to evaluate : 1.729 Fit side-chains REVERT: C 421 CYS cc_start: 0.7947 (m) cc_final: 0.7455 (m) REVERT: C 436 TYR cc_start: 0.8158 (p90) cc_final: 0.7653 (p90) REVERT: C 492 MET cc_start: 0.9096 (ttp) cc_final: 0.8826 (ttm) REVERT: C 501 LYS cc_start: 0.8171 (tmtt) cc_final: 0.7949 (tttm) REVERT: C 638 GLN cc_start: 0.8415 (pp30) cc_final: 0.7672 (pp30) REVERT: D 523 TYR cc_start: 0.7880 (m-10) cc_final: 0.7647 (m-10) REVERT: D 709 ASN cc_start: 0.8236 (t0) cc_final: 0.7935 (m-40) REVERT: B 523 TYR cc_start: 0.7876 (m-10) cc_final: 0.7640 (m-10) REVERT: B 674 MET cc_start: 0.7128 (mmm) cc_final: 0.6880 (mmm) REVERT: A 403 MET cc_start: 0.6772 (mtm) cc_final: 0.6351 (mtm) REVERT: A 421 CYS cc_start: 0.7996 (m) cc_final: 0.7550 (m) REVERT: A 436 TYR cc_start: 0.8162 (p90) cc_final: 0.7719 (p90) REVERT: A 492 MET cc_start: 0.9089 (ttp) cc_final: 0.8812 (ttm) REVERT: A 501 LYS cc_start: 0.8178 (tmtt) cc_final: 0.7935 (tttm) REVERT: A 523 MET cc_start: 0.8485 (mmm) cc_final: 0.8210 (mmm) REVERT: A 638 GLN cc_start: 0.8424 (pp30) cc_final: 0.7735 (pp30) outliers start: 24 outliers final: 21 residues processed: 192 average time/residue: 0.2780 time to fit residues: 79.7581 Evaluate side-chains 181 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 160 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 23 LEU Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 807 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 142 optimal weight: 0.1980 chunk 78 optimal weight: 0.9990 chunk 163 optimal weight: 3.9990 chunk 132 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 97 optimal weight: 0.5980 chunk 171 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 710 GLN C 752 GLN D 709 ASN A 710 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16282 Z= 0.174 Angle : 0.457 12.594 21944 Z= 0.232 Chirality : 0.039 0.234 2416 Planarity : 0.003 0.055 2658 Dihedral : 12.087 93.469 2702 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.23 % Allowed : 12.56 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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: 1.10 (0.20), residues: 1980 helix: 2.21 (0.16), residues: 1084 sheet: -1.72 (0.40), residues: 162 loop : -0.98 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 766 HIS 0.004 0.001 HIS A 548 PHE 0.011 0.001 PHE D 584 TYR 0.018 0.001 TYR C 812 ARG 0.003 0.000 ARG B 485 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 170 time to evaluate : 1.931 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 421 CYS cc_start: 0.7980 (m) cc_final: 0.7500 (m) REVERT: C 436 TYR cc_start: 0.8286 (p90) cc_final: 0.7725 (p90) REVERT: C 492 MET cc_start: 0.9145 (ttp) cc_final: 0.8882 (ttm) REVERT: C 501 LYS cc_start: 0.8145 (tmtt) cc_final: 0.7937 (tttm) REVERT: C 638 GLN cc_start: 0.8403 (pp30) cc_final: 0.7549 (pp30) REVERT: D 523 TYR cc_start: 0.7896 (m-10) cc_final: 0.7680 (m-10) REVERT: B 523 TYR cc_start: 0.7899 (m-10) cc_final: 0.7681 (m-10) REVERT: A 421 CYS cc_start: 0.7978 (m) cc_final: 0.7536 (m) REVERT: A 436 TYR cc_start: 0.8253 (p90) cc_final: 0.7678 (p90) REVERT: A 492 MET cc_start: 0.9138 (ttp) cc_final: 0.8865 (ttm) REVERT: A 501 LYS cc_start: 0.8148 (tmtt) cc_final: 0.7928 (tttm) REVERT: A 523 MET cc_start: 0.8464 (mmm) cc_final: 0.8233 (mmm) REVERT: A 638 GLN cc_start: 0.8424 (pp30) cc_final: 0.7534 (pp30) REVERT: A 803 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7632 (mtt) outliers start: 35 outliers final: 26 residues processed: 193 average time/residue: 0.2922 time to fit residues: 83.3437 Evaluate side-chains 188 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 161 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 23 LEU Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 803 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 9.9990 chunk 172 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 191 optimal weight: 0.9990 chunk 159 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 63 optimal weight: 0.0870 chunk 100 optimal weight: 0.9980 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 710 GLN A 710 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16282 Z= 0.169 Angle : 0.441 10.572 21944 Z= 0.225 Chirality : 0.038 0.232 2416 Planarity : 0.003 0.055 2658 Dihedral : 11.755 89.518 2702 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.98 % Allowed : 13.39 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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: 1.15 (0.20), residues: 1980 helix: 2.26 (0.16), residues: 1084 sheet: -1.67 (0.39), residues: 172 loop : -0.97 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 766 HIS 0.003 0.001 HIS A 548 PHE 0.011 0.001 PHE D 584 TYR 0.017 0.001 TYR C 812 ARG 0.002 0.000 ARG A 449 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 169 time to evaluate : 1.741 Fit side-chains revert: symmetry clash REVERT: C 421 CYS cc_start: 0.8008 (m) cc_final: 0.7535 (m) REVERT: C 492 MET cc_start: 0.9155 (ttp) cc_final: 0.8899 (ttm) REVERT: C 638 GLN cc_start: 0.8389 (pp30) cc_final: 0.7511 (pp30) REVERT: D 523 TYR cc_start: 0.7910 (m-10) cc_final: 0.7708 (m-10) REVERT: B 523 TYR cc_start: 0.7911 (m-10) cc_final: 0.7709 (m-10) REVERT: A 421 CYS cc_start: 0.7950 (m) cc_final: 0.7615 (m) REVERT: A 492 MET cc_start: 0.9147 (ttp) cc_final: 0.8882 (ttm) REVERT: A 501 LYS cc_start: 0.8139 (tmtt) cc_final: 0.7937 (tttm) REVERT: A 523 MET cc_start: 0.8445 (mmm) cc_final: 0.8207 (mmm) outliers start: 31 outliers final: 27 residues processed: 190 average time/residue: 0.2954 time to fit residues: 82.0645 Evaluate side-chains 183 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 156 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 23 LEU Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 719 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 109 optimal weight: 0.7980 chunk 139 optimal weight: 0.0970 chunk 108 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 chunk 106 optimal weight: 0.0570 chunk 190 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 710 GLN A 710 GLN A 752 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16282 Z= 0.144 Angle : 0.426 10.870 21944 Z= 0.218 Chirality : 0.038 0.223 2416 Planarity : 0.003 0.055 2658 Dihedral : 11.315 86.999 2702 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.66 % Allowed : 13.97 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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: 1.24 (0.20), residues: 1980 helix: 2.35 (0.16), residues: 1084 sheet: -1.61 (0.39), residues: 172 loop : -0.95 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 766 HIS 0.003 0.001 HIS A 548 PHE 0.009 0.001 PHE D 584 TYR 0.019 0.001 TYR A 812 ARG 0.002 0.000 ARG C 739 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 165 time to evaluate : 1.998 Fit side-chains revert: symmetry clash REVERT: C 421 CYS cc_start: 0.7964 (m) cc_final: 0.7472 (m) REVERT: C 436 TYR cc_start: 0.8377 (p90) cc_final: 0.8061 (p90) REVERT: C 492 MET cc_start: 0.9154 (ttp) cc_final: 0.8890 (ttm) REVERT: D 674 MET cc_start: 0.7214 (mmm) cc_final: 0.6900 (mmm) REVERT: A 421 CYS cc_start: 0.7932 (m) cc_final: 0.7594 (m) REVERT: A 492 MET cc_start: 0.9147 (ttp) cc_final: 0.8890 (ttm) REVERT: A 523 MET cc_start: 0.8459 (mmm) cc_final: 0.8235 (mmm) outliers start: 26 outliers final: 22 residues processed: 185 average time/residue: 0.2935 time to fit residues: 80.5949 Evaluate side-chains 178 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 156 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 23 LEU Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 719 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 94 optimal weight: 0.0170 chunk 17 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16282 Z= 0.158 Angle : 0.444 10.899 21944 Z= 0.223 Chirality : 0.038 0.224 2416 Planarity : 0.003 0.054 2658 Dihedral : 11.190 89.687 2702 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.17 % Allowed : 13.39 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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: 1.25 (0.20), residues: 1980 helix: 2.33 (0.16), residues: 1088 sheet: -1.57 (0.39), residues: 172 loop : -0.92 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 766 HIS 0.003 0.001 HIS A 548 PHE 0.010 0.001 PHE B 495 TYR 0.019 0.001 TYR C 812 ARG 0.002 0.000 ARG A 739 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 164 time to evaluate : 1.853 Fit side-chains revert: symmetry clash REVERT: C 421 CYS cc_start: 0.7988 (m) cc_final: 0.7519 (m) REVERT: C 492 MET cc_start: 0.9165 (ttp) cc_final: 0.8899 (ttm) REVERT: C 523 MET cc_start: 0.8385 (mmm) cc_final: 0.8178 (mmm) REVERT: D 674 MET cc_start: 0.7279 (mmm) cc_final: 0.6957 (mmm) REVERT: A 421 CYS cc_start: 0.7954 (m) cc_final: 0.7610 (m) REVERT: A 523 MET cc_start: 0.8459 (mmm) cc_final: 0.8234 (mmm) outliers start: 34 outliers final: 26 residues processed: 188 average time/residue: 0.2762 time to fit residues: 77.2816 Evaluate side-chains 178 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 152 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 23 LEU Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 719 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 0.6980 chunk 182 optimal weight: 0.9990 chunk 166 optimal weight: 0.7980 chunk 177 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 139 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16282 Z= 0.184 Angle : 0.457 11.153 21944 Z= 0.231 Chirality : 0.039 0.229 2416 Planarity : 0.003 0.055 2658 Dihedral : 11.174 87.918 2702 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.04 % Allowed : 13.58 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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: 1.21 (0.20), residues: 1980 helix: 2.27 (0.16), residues: 1088 sheet: -1.52 (0.39), residues: 172 loop : -0.92 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 766 HIS 0.004 0.001 HIS I 83 PHE 0.010 0.001 PHE B 584 TYR 0.019 0.001 TYR C 812 ARG 0.002 0.000 ARG A 739 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 151 time to evaluate : 1.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 421 CYS cc_start: 0.8009 (m) cc_final: 0.7540 (m) REVERT: C 523 MET cc_start: 0.8347 (mmm) cc_final: 0.8144 (mmm) REVERT: D 414 MET cc_start: 0.7450 (ptm) cc_final: 0.7083 (ppp) REVERT: D 674 MET cc_start: 0.7288 (mmm) cc_final: 0.6965 (mmm) REVERT: A 421 CYS cc_start: 0.7952 (m) cc_final: 0.7625 (m) REVERT: A 523 MET cc_start: 0.8435 (mmm) cc_final: 0.8219 (mmm) outliers start: 32 outliers final: 28 residues processed: 172 average time/residue: 0.2913 time to fit residues: 74.0000 Evaluate side-chains 173 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 145 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 23 LEU Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 719 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 89 optimal weight: 0.3980 chunk 130 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 121 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16282 Z= 0.288 Angle : 0.513 11.984 21944 Z= 0.259 Chirality : 0.040 0.255 2416 Planarity : 0.004 0.057 2658 Dihedral : 11.811 88.211 2702 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.85 % Allowed : 13.84 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.20), residues: 1980 helix: 2.06 (0.16), residues: 1088 sheet: -1.44 (0.43), residues: 144 loop : -1.02 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 766 HIS 0.005 0.001 HIS J 83 PHE 0.014 0.002 PHE A 491 TYR 0.020 0.002 TYR C 812 ARG 0.003 0.000 ARG A 449 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 145 time to evaluate : 1.675 Fit side-chains revert: symmetry clash REVERT: C 421 CYS cc_start: 0.8037 (m) cc_final: 0.7803 (m) outliers start: 29 outliers final: 24 residues processed: 165 average time/residue: 0.3106 time to fit residues: 74.8447 Evaluate side-chains 164 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 140 time to evaluate : 2.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 23 LEU Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 719 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 144 optimal weight: 0.3980 chunk 23 optimal weight: 2.9990 chunk 43 optimal weight: 0.0070 chunk 157 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 161 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 138 optimal weight: 1.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 714 GLN J 183 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.159608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.123963 restraints weight = 20030.411| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.70 r_work: 0.3081 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.4867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16282 Z= 0.155 Angle : 0.449 11.532 21944 Z= 0.227 Chirality : 0.038 0.216 2416 Planarity : 0.003 0.054 2658 Dihedral : 11.196 87.492 2702 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.66 % Allowed : 14.03 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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: 1.19 (0.20), residues: 1980 helix: 2.21 (0.17), residues: 1088 sheet: -1.28 (0.44), residues: 140 loop : -0.96 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 766 HIS 0.003 0.001 HIS A 548 PHE 0.010 0.001 PHE B 584 TYR 0.019 0.001 TYR C 812 ARG 0.002 0.000 ARG A 739 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3226.55 seconds wall clock time: 59 minutes 32.53 seconds (3572.53 seconds total)