Starting phenix.real_space_refine on Sat Feb 17 01:46:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ocf_12806/02_2024/7ocf_12806_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ocf_12806/02_2024/7ocf_12806.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ocf_12806/02_2024/7ocf_12806.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ocf_12806/02_2024/7ocf_12806.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ocf_12806/02_2024/7ocf_12806_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ocf_12806/02_2024/7ocf_12806_updated.pdb" } resolution = 3.6 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: 5 Type Number sf(0) Gaussians S 104 5.16 5 Cl 4 4.86 5 C 11320 2.51 5 N 2710 2.21 5 O 2950 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "A ASP 486": "OD1" <-> "OD2" Residue "A PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 541": "NH1" <-> "NH2" Residue "A PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 546": "OE1" <-> "OE2" Residue "A GLU 566": "OE1" <-> "OE2" Residue "A PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 711": "NH1" <-> "NH2" Residue "A ASP 715": "OD1" <-> "OD2" Residue "A TYR 793": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 422": "OE1" <-> "OE2" Residue "B TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 519": "OD1" <-> "OD2" Residue "B GLU 524": "OE1" <-> "OE2" Residue "B PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 586": "NH1" <-> "NH2" Residue "B PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 755": "OE1" <-> "OE2" Residue "B TYR 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 813": "OE1" <-> "OE2" Residue "G ARG 35": "NH1" <-> "NH2" Residue "G ARG 65": "NH1" <-> "NH2" Residue "G TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 87": "OE1" <-> "OE2" Residue "G TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 48": "NH1" <-> "NH2" Residue "I ARG 88": "NH1" <-> "NH2" 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 232": "OE1" <-> "OE2" Residue "C TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 483": "OE1" <-> "OE2" Residue "C ASP 486": "OD1" <-> "OD2" Residue "C PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 541": "NH1" <-> "NH2" Residue "C PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 546": "OE1" <-> "OE2" Residue "C GLU 566": "OE1" <-> "OE2" Residue "C PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 711": "NH1" <-> "NH2" Residue "C ASP 715": "OD1" <-> "OD2" Residue "C TYR 793": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 35": "NH1" <-> "NH2" Residue "E ARG 65": "NH1" <-> "NH2" Residue "E TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 87": "OE1" <-> "OE2" Residue "E TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 48": "NH1" <-> "NH2" Residue "J ARG 88": "NH1" <-> "NH2" 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 232": "OE1" <-> "OE2" Residue "D TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 422": "OE1" <-> "OE2" Residue "D TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 519": "OD1" <-> "OD2" Residue "D GLU 524": "OE1" <-> "OE2" Residue "D PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 586": "NH1" <-> "NH2" Residue "D PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 755": "OE1" <-> "OE2" Residue "D TYR 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 813": "OE1" <-> "OE2" Residue "A GLU 1408": "OE1" <-> "OE2" Residue "B GLU 1407": "OE1" <-> "OE2" Residue "C GLU 1408": "OE1" <-> "OE2" Residue "D GLU 1406": "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: 17088 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 2803 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 391} Chain breaks: 2 Unresolved non-hydrogen bonds: 403 Unresolved non-hydrogen angles: 483 Unresolved non-hydrogen dihedrals: 338 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 23, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 220 Chain: "B" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2878 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 385} Chain breaks: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 207 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 131 Chain: "G" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1222 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ASN:plan1': 3, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 64 Chain: "I" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1322 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 2, 'TRANS': 181} Chain breaks: 2 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 4, 'HIS:plan': 2, 'ARG:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 65 Chain: "C" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 2803 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 391} Chain breaks: 2 Unresolved non-hydrogen bonds: 403 Unresolved non-hydrogen angles: 483 Unresolved non-hydrogen dihedrals: 338 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 23, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 220 Chain: "E" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1222 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ASN:plan1': 3, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 64 Chain: "J" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1322 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 2, 'TRANS': 181} Chain breaks: 2 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 4, 'HIS:plan': 2, 'ARG:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 65 Chain: "D" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2878 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 385} Chain breaks: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 207 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 131 Chain: "A" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 147 Unusual residues: {'CYZ': 1, 'PC1': 6} Classifications: {'peptide': 1, 'undetermined': 7} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PC1:plan-2': 6} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 132 Unusual residues: {'CYZ': 1, 'PC1': 5} Classifications: {'peptide': 1, 'undetermined': 6} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PC1:plan-2': 4, 'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 19 Chain: "I" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 147 Unusual residues: {'CYZ': 1, 'PC1': 6} Classifications: {'peptide': 1, 'undetermined': 7} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PC1:plan-2': 6} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PC1:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 114 Unusual residues: {'CYZ': 1, 'PC1': 4} Classifications: {'peptide': 1, 'undetermined': 5} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-2': 3, 'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 9.39, per 1000 atoms: 0.55 Number of scatterers: 17088 At special positions: 0 Unit cell: (116.63, 112.35, 146.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 104 16.00 O 2950 8.00 N 2710 7.00 C 11320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 714 " - pdb=" SG CYS A 769 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 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 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 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.44 Conformation dependent library (CDL) restraints added in 3.2 seconds 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4228 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 88 helices and 10 sheets defined 53.1% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.02 Creating SS restraints... Processing helix chain 'A' and resid 414 through 416 No H-bonds generated for 'chain 'A' and resid 414 through 416' Processing helix chain 'A' and resid 420 through 432 Processing helix chain 'A' and resid 459 through 464 Processing helix chain 'A' and resid 479 through 482 No H-bonds generated for 'chain 'A' and resid 479 through 482' Processing helix chain 'A' and resid 512 through 514 No H-bonds generated for 'chain 'A' and resid 512 through 514' Processing helix chain 'A' and resid 519 through 541 Processing helix chain 'A' and resid 544 through 547 No H-bonds generated for 'chain 'A' and resid 544 through 547' Processing helix chain 'A' and resid 570 through 580 Processing helix chain 'A' and resid 592 through 620 removed outlier: 4.090A pdb=" N VAL A 597 " --> pdb=" O SER A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 637 Processing helix chain 'A' and resid 650 through 657 Processing helix chain 'A' and resid 661 through 671 Processing helix chain 'A' and resid 682 through 691 Processing helix chain 'A' and resid 704 through 709 Processing helix chain 'A' and resid 740 through 751 Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 785 through 814 removed outlier: 3.704A pdb=" N ALA A 789 " --> pdb=" O SER A 786 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N GLY A 790 " --> pdb=" O ASN A 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'B' and resid 424 through 436 removed outlier: 3.738A pdb=" N HIS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 468 removed outlier: 3.598A 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 545 Processing helix chain 'B' and resid 574 through 584 Processing helix chain 'B' and resid 596 through 617 removed outlier: 4.120A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 625 Processing helix chain 'B' and resid 636 through 641 Processing helix chain 'B' and resid 654 through 660 Processing helix chain 'B' and resid 665 through 675 Processing helix chain 'B' and resid 686 through 695 Processing helix chain 'B' and resid 707 through 714 Processing helix chain 'B' and resid 742 through 755 Processing helix chain 'B' and resid 758 through 766 Processing helix chain 'B' and resid 793 through 818 Processing helix chain 'G' and resid 5 through 39 removed outlier: 3.717A pdb=" N SER G 19 " --> pdb=" O VAL G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 84 removed outlier: 3.793A pdb=" N LEU G 54 " --> pdb=" O ALA G 50 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL G 68 " --> pdb=" O LEU G 64 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VAL G 69 " --> pdb=" O ARG G 65 " (cutoff:3.500A) Proline residue: G 70 - end of helix Processing helix chain 'G' and resid 89 through 106 Proline residue: G 96 - end of helix Processing helix chain 'G' and resid 125 through 158 Processing helix chain 'I' and resid 20 through 41 Processing helix chain 'I' and resid 112 through 114 No H-bonds generated for 'chain 'I' and resid 112 through 114' Processing helix chain 'I' and resid 116 through 127 Processing helix chain 'I' and resid 129 through 149 removed outlier: 3.755A pdb=" N ARG I 149 " --> pdb=" O VAL I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 156 through 185 Processing helix chain 'I' and resid 203 through 232 Processing helix chain 'C' and resid 414 through 416 No H-bonds generated for 'chain 'C' and resid 414 through 416' Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 459 through 464 Processing helix chain 'C' and resid 479 through 482 No H-bonds generated for 'chain 'C' and resid 479 through 482' Processing helix chain 'C' and resid 512 through 514 No H-bonds generated for 'chain 'C' and resid 512 through 514' Processing helix chain 'C' and resid 519 through 541 Processing helix chain 'C' and resid 544 through 547 No H-bonds generated for 'chain 'C' and resid 544 through 547' Processing helix chain 'C' and resid 570 through 580 Processing helix chain 'C' and resid 592 through 620 removed outlier: 4.083A pdb=" N VAL C 597 " --> pdb=" O SER C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 637 Processing helix chain 'C' and resid 650 through 657 Processing helix chain 'C' and resid 661 through 671 Processing helix chain 'C' and resid 682 through 691 Processing helix chain 'C' and resid 704 through 709 Processing helix chain 'C' and resid 740 through 751 Processing helix chain 'C' and resid 754 through 763 Processing helix chain 'C' and resid 785 through 814 removed outlier: 3.701A pdb=" N ALA C 789 " --> pdb=" O SER C 786 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N GLY C 790 " --> pdb=" O ASN C 787 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 39 removed outlier: 3.717A pdb=" N SER E 19 " --> pdb=" O VAL E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 84 removed outlier: 3.793A pdb=" N LEU E 54 " --> pdb=" O ALA E 50 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL E 68 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VAL E 69 " --> pdb=" O ARG E 65 " (cutoff:3.500A) Proline residue: E 70 - end of helix Processing helix chain 'E' and resid 89 through 106 Proline residue: E 96 - end of helix Processing helix chain 'E' and resid 125 through 158 Processing helix chain 'J' and resid 20 through 41 Processing helix chain 'J' and resid 112 through 114 No H-bonds generated for 'chain 'J' and resid 112 through 114' Processing helix chain 'J' and resid 116 through 127 Processing helix chain 'J' and resid 129 through 149 removed outlier: 3.755A pdb=" N ARG J 149 " --> pdb=" O VAL J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 156 through 185 Processing helix chain 'J' and resid 203 through 232 Processing helix chain 'D' and resid 412 through 414 No H-bonds generated for 'chain 'D' and resid 412 through 414' Processing helix chain 'D' and resid 417 through 419 No H-bonds generated for 'chain 'D' and resid 417 through 419' Processing helix chain 'D' and resid 424 through 436 removed outlier: 3.738A pdb=" N HIS D 435 " --> pdb=" O GLU D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 468 removed outlier: 3.598A 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 545 Processing helix chain 'D' and resid 574 through 584 Processing helix chain 'D' and resid 596 through 617 removed outlier: 4.120A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 625 Processing helix chain 'D' and resid 636 through 641 Processing helix chain 'D' and resid 654 through 660 Processing helix chain 'D' and resid 665 through 675 Processing helix chain 'D' and resid 686 through 695 Processing helix chain 'D' and resid 707 through 714 Processing helix chain 'D' and resid 742 through 755 Processing helix chain 'D' and resid 758 through 766 Processing helix chain 'D' and resid 793 through 818 Processing sheet with id= A, first strand: chain 'A' and resid 716 through 719 removed outlier: 4.128A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LYS A 501 " --> pdb=" O TYR A 696 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N TYR A 696 " --> pdb=" O LYS A 501 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ALA A 642 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N LEU A 699 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N GLY A 644 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 9.525A pdb=" N GLU A 701 " --> pdb=" O GLY A 644 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 397 through 399 Processing sheet with id= C, first strand: chain 'B' and resid 501 through 503 removed outlier: 6.867A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'I' and resid 80 through 84 Processing sheet with id= E, first strand: chain 'I' and resid 88 through 90 Processing sheet with id= F, first strand: chain 'C' and resid 716 through 719 removed outlier: 4.130A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LYS C 501 " --> pdb=" O TYR C 696 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N TYR C 696 " --> pdb=" O LYS C 501 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 9.525A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 80 through 84 Processing sheet with id= H, first strand: chain 'J' and resid 88 through 90 Processing sheet with id= I, first strand: chain 'D' and resid 397 through 399 Processing sheet with id= J, first strand: chain 'D' and resid 501 through 503 removed outlier: 6.867A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) 892 hydrogen bonds defined for protein. 2508 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: 4.68 Time building geometry restraints manager: 7.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.99 - 1.16: 12 1.16 - 1.33: 3091 1.33 - 1.50: 7476 1.50 - 1.67: 6717 1.67 - 1.83: 166 Bond restraints: 17462 Sorted by residual: bond pdb=" C2 CYZ C1401 " pdb=" C3 CYZ C1401 " ideal model delta sigma weight residual 1.513 0.990 0.523 2.00e-02 2.50e+03 6.83e+02 bond pdb=" C2 CYZ A1401 " pdb=" C3 CYZ A1401 " ideal model delta sigma weight residual 1.513 0.991 0.522 2.00e-02 2.50e+03 6.81e+02 bond pdb=" C2 CYZ B1401 " pdb=" C3 CYZ B1401 " ideal model delta sigma weight residual 1.513 0.996 0.517 2.00e-02 2.50e+03 6.70e+02 bond pdb=" C2 CYZ D1401 " pdb=" C3 CYZ D1401 " ideal model delta sigma weight residual 1.513 0.996 0.517 2.00e-02 2.50e+03 6.69e+02 bond pdb=" C4 CYZ C1401 " pdb=" C5 CYZ C1401 " ideal model delta sigma weight residual 1.512 1.072 0.440 2.00e-02 2.50e+03 4.85e+02 ... (remaining 17457 not shown) Histogram of bond angle deviations from ideal: 86.35 - 95.90: 14 95.90 - 105.44: 268 105.44 - 114.99: 10579 114.99 - 124.54: 12518 124.54 - 134.08: 319 Bond angle restraints: 23698 Sorted by residual: angle pdb=" CD LYS I 102 " pdb=" CE LYS I 102 " pdb=" NZ LYS I 102 " ideal model delta sigma weight residual 111.90 86.35 25.55 3.20e+00 9.77e-02 6.38e+01 angle pdb=" CD LYS J 102 " pdb=" CE LYS J 102 " pdb=" NZ LYS J 102 " ideal model delta sigma weight residual 111.90 86.41 25.49 3.20e+00 9.77e-02 6.35e+01 angle pdb=" O3 CYZ B1401 " pdb=" S2 CYZ B1401 " pdb=" O4 CYZ B1401 " ideal model delta sigma weight residual 118.35 101.03 17.32 3.00e+00 1.11e-01 3.33e+01 angle pdb=" O3 CYZ D1401 " pdb=" S2 CYZ D1401 " pdb=" O4 CYZ D1401 " ideal model delta sigma weight residual 118.35 101.08 17.27 3.00e+00 1.11e-01 3.31e+01 angle pdb=" O3 CYZ C1401 " pdb=" S2 CYZ C1401 " pdb=" O4 CYZ C1401 " ideal model delta sigma weight residual 118.35 101.12 17.23 3.00e+00 1.11e-01 3.30e+01 ... (remaining 23693 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.78: 9535 21.78 - 43.55: 511 43.55 - 65.33: 80 65.33 - 87.10: 22 87.10 - 108.88: 10 Dihedral angle restraints: 10158 sinusoidal: 3550 harmonic: 6608 Sorted by residual: dihedral pdb=" N2 CYZ B1401 " pdb=" C8 CYZ B1401 " pdb=" N1 CYZ B1401 " pdb=" S1 CYZ B1401 " ideal model delta sinusoidal sigma weight residual 55.73 -53.15 108.88 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" N2 CYZ D1401 " pdb=" C8 CYZ D1401 " pdb=" N1 CYZ D1401 " pdb=" S1 CYZ D1401 " ideal model delta sinusoidal sigma weight residual 55.73 -53.12 108.85 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" C1 CYZ B1401 " pdb=" C8 CYZ B1401 " pdb=" N1 CYZ B1401 " pdb=" S1 CYZ B1401 " ideal model delta sinusoidal sigma weight residual -71.23 -175.51 104.28 1 3.00e+01 1.11e-03 1.33e+01 ... (remaining 10155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.393: 2722 0.393 - 0.785: 8 0.785 - 1.178: 0 1.178 - 1.570: 4 1.570 - 1.963: 4 Chirality restraints: 2738 Sorted by residual: chirality pdb=" C2 CYZ C1401 " pdb=" C1 CYZ C1401 " pdb=" C3 CYZ C1401 " pdb=" C7 CYZ C1401 " both_signs ideal model delta sigma weight residual False 3.31 1.35 1.96 2.00e-01 2.50e+01 9.63e+01 chirality pdb=" C2 CYZ A1401 " pdb=" C1 CYZ A1401 " pdb=" C3 CYZ A1401 " pdb=" C7 CYZ A1401 " both_signs ideal model delta sigma weight residual False 3.31 1.35 1.96 2.00e-01 2.50e+01 9.63e+01 chirality pdb=" C2 CYZ B1401 " pdb=" C1 CYZ B1401 " pdb=" C3 CYZ B1401 " pdb=" C7 CYZ B1401 " both_signs ideal model delta sigma weight residual False 3.31 1.35 1.96 2.00e-01 2.50e+01 9.57e+01 ... (remaining 2735 not shown) Planarity restraints: 2886 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 403 " 0.038 5.00e-02 4.00e+02 5.75e-02 5.30e+00 pdb=" N PRO B 404 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 404 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 404 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 403 " -0.038 5.00e-02 4.00e+02 5.73e-02 5.26e+00 pdb=" N PRO D 404 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 404 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 404 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 399 " -0.030 5.00e-02 4.00e+02 4.56e-02 3.32e+00 pdb=" N PRO C 400 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 400 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 400 " -0.022 5.00e-02 4.00e+02 ... (remaining 2883 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 171 2.63 - 3.20: 16760 3.20 - 3.77: 25559 3.77 - 4.33: 34110 4.33 - 4.90: 57562 Nonbonded interactions: 134162 Sorted by model distance: nonbonded pdb=" O TYR I 43 " pdb=" OG SER I 204 " model vdw 2.067 2.440 nonbonded pdb=" O TYR J 43 " pdb=" OG SER J 204 " model vdw 2.067 2.440 nonbonded pdb=" N GLU B 705 " pdb=" OE1 GLU B 705 " model vdw 2.095 2.520 nonbonded pdb=" N GLU D 705 " pdb=" OE1 GLU D 705 " model vdw 2.095 2.520 nonbonded pdb=" O GLY C 568 " pdb=" OG SER C 572 " model vdw 2.106 2.440 ... (remaining 134157 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 and (name N or name CA or name C or name \ O or name CB )) or resid 400 through 403 or resid 405 through 407 or resid 412 t \ hrough 414 or resid 416 through 422 or resid 424 through 431 or resid 433 or res \ id 436 or resid 438 or resid 440 through 441 or resid 443 through 450 or (resid \ 452 through 454 and (name N or name CA or name C or name O or name CB )) or resi \ d 456 through 466 or (resid 468 through 469 and (name N or name CA or name C or \ name O or name CB )) or resid 471 or resid 473 through 478 or (resid 479 and (na \ me N or name CA or name C or name O or name CB )) or resid 480 through 485 or (r \ esid 486 and (name N or name CA or name C or name O or name CB )) or resid 487 t \ hrough 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 628 or (resid 629 th \ rough 630 and (name N or name CA or name C or name O or name CB )) or resid 631 \ through 635 or resid 637 through 646 or resid 649 through 656 or (resid 657 and \ (name N or name CA or name C or name O or name CB )) or resid 658 through 663 or \ resid 665 through 668 or (resid 669 through 670 and (name N or name CA or name \ C or name O or name CB )) or resid 672 through 675 or (resid 676 and (name N or \ name CA or name C or name O or name CB )) or resid 677 through 682 or resid 684 \ through 685 or resid 688 through 690 or (resid 691 and (name N or name CA or nam \ e C or name O or name CB )) or resid 692 through 714 or (resid 715 and (name N o \ r name CA or name C or name O or name CB )) or resid 716 through 736 or resid 73 \ 8 or resid 741 or (resid 742 and (name N or name CA or name C or name O or name \ CB )) or resid 743 through 753 or (resid 754 and (name N or name CA or name C or \ name O or name CB )) or resid 755 through 758 or (resid 759 and (name N or name \ CA or name C or name O or name CB )) or resid 761 through 783 or (resid 784 and \ (name N or name CA or name C or name O or name CB )) or resid 785 through 795 o \ r resid 797 through 815 or resid 1401 or (resid 1402 and (name C21 or name C22 o \ r name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C \ 29 or name C2A or name C2B or name C2C or name C2D or name C2E or name O21 or na \ me O22)) or resid 1403 through 1404 or resid 1408)) selection = (chain 'B' and ((resid 397 through 402 and (name N or name CA or name C or name \ O or name CB )) or resid 404 through 405 or (resid 406 through 407 and (name N o \ r name CA or name C or name O or name CB )) or (resid 409 through 411 and (name \ N or name CA or name C or name O or name CB )) or resid 416 through 418 or (resi \ d 420 and (name N or name CA or name C or name O or name CB )) or resid 421 or ( \ resid 422 and (name N or name CA or name C or name O or name CB )) or resid 423 \ through 424 or (resid 425 through 426 and (name N or name CA or name C or name O \ or name CB )) or resid 428 through 434 or (resid 435 and (name N or name CA or \ name C or name O or name CB )) or resid 437 or resid 440 or resid 442 or resid 4 \ 44 through 445 or (resid 447 and (name N or name CA or name C or name O or name \ CB )) or resid 448 or (resid 449 and (name N or name CA or name C or name O or n \ ame CB )) or resid 450 through 452 or (resid 453 through 454 and (name N or name \ CA or name C or name O or name CB )) or resid 456 through 458 or resid 460 thro \ ugh 462 or (resid 463 and (name N or name CA or name C or name O or name CB )) o \ r resid 464 through 466 or (resid 467 and (name N or name CA or name C or name O \ or name CB )) or resid 468 through 470 or resid 472 through 473 or resid 475 or \ resid 477 through 480 or (resid 481 and (name N or name CA or name C or name O \ or name CB )) or resid 482 through 504 or (resid 505 through 506 and (name N or \ name CA or name C or name O or name CB )) or resid 507 or (resid 508 through 511 \ and (name N or name CA or name C or name O or name CB )) or resid 512 through 5 \ 85 or resid 587 through 625 or (resid 626 through 631 and (name N or name CA or \ name C or name O or name CB )) or resid 632 through 637 or (resid 638 through 63 \ 9 and (name N or name CA or name C or name O or name CB )) or (resid 641 through \ 642 and (name N or name CA or name C or name O or name CB )) or resid 643 throu \ gh 648 or (resid 649 and (name N or name CA or name C or name O or name CB )) or \ resid 650 or resid 653 through 663 or (resid 664 through 665 and (name N or nam \ e CA or name C or name O or name CB )) or resid 666 through 667 or (resid 669 th \ rough 670 and (name N or name CA or name C or name O or name CB )) or resid 671 \ or (resid 672 through 674 and (name N or name CA or name C or name O or name CB \ )) or (resid 676 through 678 and (name N or name CA or name C or name O or name \ CB )) or resid 679 through 684 or (resid 685 and (name N or name CA or name C or \ name O or name CB )) or resid 686 or resid 688 through 689 or (resid 692 and (n \ ame N or name CA or name C or name O or name CB )) or resid 693 through 704 or ( \ resid 705 and (name N or name CA or name C or name O or name CB )) or resid 706 \ through 712 or (resid 713 and (name N or name CA or name C or name O or name CB \ )) or resid 714 through 739 or (resid 740 and (name N or name CA or name C or na \ me O or name CB )) or (resid 742 and (name N or name CA or name C or name O or n \ ame CB )) or resid 745 through 751 or (resid 752 and (name N or name CA or name \ C or name O or name CB )) or resid 753 through 759 or (resid 760 through 761 and \ (name N or name CA or name C or name O or name CB )) or resid 762 through 763 o \ r (resid 765 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 66 through 774 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 812 or (resid 813 and (name \ N or name CA or name C or name O or name CB )) or resid 814 through 816 or (resi \ d 817 through 819 and (name N or name CA or name C or name O or name CB )) or re \ sid 1401 through 1402 or (resid 1403 through 1404 and (name C21 or name C22 or n \ ame C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name C2A or name C2B or name C2C or name C2D or name C2E or name C2F or name \ C2G or name O21 or name O22)) or resid 1407)) selection = (chain 'C' and ((resid 393 through 398 and (name N or name CA or name C or name \ O or name CB )) or resid 400 through 403 or resid 405 through 407 or resid 412 t \ hrough 414 or resid 416 through 422 or resid 424 through 431 or resid 433 or res \ id 436 or resid 438 or resid 440 through 441 or resid 443 through 450 or (resid \ 452 through 454 and (name N or name CA or name C or name O or name CB )) or resi \ d 456 through 466 or (resid 468 through 469 and (name N or name CA or name C or \ name O or name CB )) or resid 471 or resid 473 through 478 or (resid 479 and (na \ me N or name CA or name C or name O or name CB )) or resid 480 through 485 or (r \ esid 486 and (name N or name CA or name C or name O or name CB )) or resid 487 t \ hrough 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 628 or (resid 629 th \ rough 630 and (name N or name CA or name C or name O or name CB )) or resid 631 \ through 635 or resid 637 through 646 or resid 649 through 656 or (resid 657 and \ (name N or name CA or name C or name O or name CB )) or resid 658 through 663 or \ resid 665 through 668 or (resid 669 through 670 and (name N or name CA or name \ C or name O or name CB )) or resid 672 through 675 or (resid 676 and (name N or \ name CA or name C or name O or name CB )) or resid 677 through 682 or resid 684 \ through 685 or resid 688 through 690 or (resid 691 and (name N or name CA or nam \ e C or name O or name CB )) or resid 692 through 714 or (resid 715 and (name N o \ r name CA or name C or name O or name CB )) or resid 716 through 736 or resid 73 \ 8 or resid 741 or (resid 742 and (name N or name CA or name C or name O or name \ CB )) or resid 743 through 753 or (resid 754 and (name N or name CA or name C or \ name O or name CB )) or resid 755 through 758 or (resid 759 and (name N or name \ CA or name C or name O or name CB )) or resid 761 through 783 or (resid 784 and \ (name N or name CA or name C or name O or name CB )) or resid 785 through 795 o \ r resid 797 through 815 or resid 1401 or (resid 1402 and (name C21 or name C22 o \ r name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C \ 29 or name C2A or name C2B or name C2C or name C2D or name C2E or name O21 or na \ me O22)) or resid 1403 through 1404 or resid 1408)) selection = (chain 'D' and ((resid 397 through 402 and (name N or name CA or name C or name \ O or name CB )) or resid 404 through 405 or (resid 406 through 407 and (name N o \ r name CA or name C or name O or name CB )) or (resid 409 through 411 and (name \ N or name CA or name C or name O or name CB )) or resid 416 through 418 or (resi \ d 420 and (name N or name CA or name C or name O or name CB )) or resid 421 or ( \ resid 422 and (name N or name CA or name C or name O or name CB )) or resid 423 \ through 424 or (resid 425 through 426 and (name N or name CA or name C or name O \ or name CB )) or resid 428 through 434 or (resid 435 and (name N or name CA or \ name C or name O or name CB )) or resid 437 or resid 440 or resid 442 or resid 4 \ 44 through 445 or (resid 447 and (name N or name CA or name C or name O or name \ CB )) or resid 448 or (resid 449 and (name N or name CA or name C or name O or n \ ame CB )) or resid 450 through 452 or (resid 453 through 454 and (name N or name \ CA or name C or name O or name CB )) or resid 456 through 458 or resid 460 thro \ ugh 462 or (resid 463 and (name N or name CA or name C or name O or name CB )) o \ r resid 464 through 466 or (resid 467 and (name N or name CA or name C or name O \ or name CB )) or resid 468 through 470 or resid 472 through 473 or resid 475 or \ resid 477 through 480 or (resid 481 and (name N or name CA or name C or name O \ or name CB )) or resid 482 through 504 or (resid 505 through 506 and (name N or \ name CA or name C or name O or name CB )) or resid 507 or (resid 508 through 511 \ and (name N or name CA or name C or name O or name CB )) or resid 512 through 5 \ 85 or resid 587 through 625 or (resid 626 through 631 and (name N or name CA or \ name C or name O or name CB )) or resid 632 through 637 or (resid 638 through 63 \ 9 and (name N or name CA or name C or name O or name CB )) or (resid 641 through \ 642 and (name N or name CA or name C or name O or name CB )) or resid 643 throu \ gh 648 or (resid 649 and (name N or name CA or name C or name O or name CB )) or \ resid 650 or resid 653 through 663 or (resid 664 through 665 and (name N or nam \ e CA or name C or name O or name CB )) or resid 666 through 667 or (resid 669 th \ rough 670 and (name N or name CA or name C or name O or name CB )) or resid 671 \ or (resid 672 through 674 and (name N or name CA or name C or name O or name CB \ )) or (resid 676 through 678 and (name N or name CA or name C or name O or name \ CB )) or resid 679 through 684 or (resid 685 and (name N or name CA or name C or \ name O or name CB )) or resid 686 or resid 688 through 689 or (resid 692 and (n \ ame N or name CA or name C or name O or name CB )) or resid 693 through 704 or ( \ resid 705 and (name N or name CA or name C or name O or name CB )) or resid 706 \ through 712 or (resid 713 and (name N or name CA or name C or name O or name CB \ )) or resid 714 through 739 or (resid 740 and (name N or name CA or name C or na \ me O or name CB )) or (resid 742 and (name N or name CA or name C or name O or n \ ame CB )) or resid 745 through 751 or (resid 752 and (name N or name CA or name \ C or name O or name CB )) or resid 753 through 759 or (resid 760 through 761 and \ (name N or name CA or name C or name O or name CB )) or resid 762 through 763 o \ r (resid 765 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 66 through 774 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 812 or (resid 813 and (name \ N or name CA or name C or name O or name CB )) or resid 814 through 816 or (resi \ d 817 through 819 and (name N or name CA or name C or name O or name CB )) or re \ sid 1401 through 1402 or (resid 1403 through 1404 and (name C21 or name C22 or n \ ame C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name C2A or name C2B or name C2C or name C2D or name C2E or name C2F or name \ C2G or name O21 or name O22)) or resid 1406)) } ncs_group { reference = (chain 'E' and resid 2 through 159) selection = chain 'G' } ncs_group { reference = chain 'I' selection = chain 'J' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.450 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 47.480 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.110 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 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 : 0.018 0.523 17462 Z= 1.183 Angle : 0.947 25.552 23698 Z= 0.395 Chirality : 0.109 1.963 2738 Planarity : 0.003 0.058 2886 Dihedral : 14.254 108.876 5906 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: 0.18 (0.18), residues: 2254 helix: 1.48 (0.14), residues: 1302 sheet: -1.34 (0.39), residues: 168 loop : -1.92 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 601 HIS 0.003 0.001 HIS J 83 PHE 0.015 0.002 PHE B 574 TYR 0.013 0.001 TYR B 616 ARG 0.004 0.001 ARG C 656 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 335 time to evaluate : 1.667 Fit side-chains revert: symmetry clash REVERT: A 498 ILE cc_start: 0.8015 (mt) cc_final: 0.7806 (mt) REVERT: B 628 ARG cc_start: 0.7156 (pmt-80) cc_final: 0.6929 (pmt-80) REVERT: G 35 ARG cc_start: 0.7824 (ttp-170) cc_final: 0.7314 (ttp-170) REVERT: I 22 LEU cc_start: 0.7948 (tp) cc_final: 0.7599 (mt) REVERT: I 118 GLU cc_start: 0.7676 (tp30) cc_final: 0.7351 (tp30) REVERT: E 9 CYS cc_start: 0.8100 (m) cc_final: 0.7860 (m) REVERT: J 26 ILE cc_start: 0.8398 (mm) cc_final: 0.8125 (mt) REVERT: J 118 GLU cc_start: 0.7747 (tp30) cc_final: 0.7545 (tp30) REVERT: D 407 MET cc_start: 0.6729 (mmm) cc_final: 0.6196 (mtm) outliers start: 0 outliers final: 0 residues processed: 335 average time/residue: 0.3158 time to fit residues: 153.7944 Evaluate side-chains 293 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 10.0000 chunk 169 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 90 optimal weight: 7.9990 chunk 175 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 106 optimal weight: 0.4980 chunk 130 optimal weight: 0.3980 chunk 203 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 GLN B 411 ASN C 710 GLN J 183 ASN J 197 ASN D 411 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17462 Z= 0.185 Angle : 0.517 8.179 23698 Z= 0.263 Chirality : 0.039 0.153 2738 Planarity : 0.004 0.039 2886 Dihedral : 11.245 89.989 2964 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.21 % Allowed : 9.80 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: 0.85 (0.18), residues: 2254 helix: 1.98 (0.15), residues: 1310 sheet: -0.71 (0.49), residues: 104 loop : -1.65 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 460 HIS 0.003 0.001 HIS I 105 PHE 0.020 0.001 PHE D 546 TYR 0.016 0.001 TYR C 669 ARG 0.007 0.001 ARG A 657 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 314 time to evaluate : 2.593 Fit side-chains REVERT: A 475 LEU cc_start: 0.7843 (tt) cc_final: 0.7594 (tp) REVERT: A 485 ILE cc_start: 0.8663 (tp) cc_final: 0.8356 (tp) REVERT: A 498 ILE cc_start: 0.7958 (mt) cc_final: 0.7732 (mt) REVERT: G 35 ARG cc_start: 0.7854 (ttp-170) cc_final: 0.7376 (ttp-170) REVERT: I 43 TYR cc_start: 0.7500 (OUTLIER) cc_final: 0.6736 (t80) REVERT: I 118 GLU cc_start: 0.7693 (tp30) cc_final: 0.7420 (tp30) REVERT: C 475 LEU cc_start: 0.7966 (tt) cc_final: 0.7695 (tp) REVERT: C 711 ARG cc_start: 0.7185 (mmp80) cc_final: 0.6976 (mmp80) REVERT: J 26 ILE cc_start: 0.8545 (mm) cc_final: 0.8244 (mt) REVERT: D 407 MET cc_start: 0.6599 (mmm) cc_final: 0.6271 (mtt) outliers start: 18 outliers final: 9 residues processed: 318 average time/residue: 0.3331 time to fit residues: 156.2076 Evaluate side-chains 298 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 288 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain I residue 43 TYR Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 62 CYS Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 736 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 7.9990 chunk 63 optimal weight: 7.9990 chunk 169 optimal weight: 5.9990 chunk 138 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 203 optimal weight: 2.9990 chunk 220 optimal weight: 4.9990 chunk 181 optimal weight: 0.4980 chunk 202 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 GLN C 710 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17462 Z= 0.278 Angle : 0.535 7.184 23698 Z= 0.269 Chirality : 0.040 0.198 2738 Planarity : 0.004 0.062 2886 Dihedral : 10.765 86.831 2964 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.54 % Allowed : 12.42 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: 0.71 (0.18), residues: 2254 helix: 1.81 (0.15), residues: 1314 sheet: -0.62 (0.46), residues: 124 loop : -1.65 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 766 HIS 0.003 0.001 HIS I 105 PHE 0.015 0.001 PHE E 146 TYR 0.020 0.001 TYR D 405 ARG 0.006 0.001 ARG A 657 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 316 time to evaluate : 1.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 485 ILE cc_start: 0.8716 (tp) cc_final: 0.8439 (tp) REVERT: A 498 ILE cc_start: 0.7988 (mt) cc_final: 0.7713 (mt) REVERT: A 629 ILE cc_start: 0.5579 (OUTLIER) cc_final: 0.5361 (mm) REVERT: A 747 LEU cc_start: 0.9011 (mm) cc_final: 0.8747 (mt) REVERT: B 714 GLN cc_start: 0.8348 (mm110) cc_final: 0.8124 (mm-40) REVERT: G 35 ARG cc_start: 0.7829 (ttp-170) cc_final: 0.7340 (ttp-170) REVERT: C 629 ILE cc_start: 0.5684 (OUTLIER) cc_final: 0.5366 (mm) REVERT: C 711 ARG cc_start: 0.7309 (mmp80) cc_final: 0.7076 (mmp80) REVERT: J 26 ILE cc_start: 0.8634 (mm) cc_final: 0.8287 (mt) REVERT: J 43 TYR cc_start: 0.7410 (OUTLIER) cc_final: 0.6501 (t80) REVERT: D 435 HIS cc_start: 0.6677 (m90) cc_final: 0.6388 (m90) outliers start: 23 outliers final: 17 residues processed: 328 average time/residue: 0.3161 time to fit residues: 152.9168 Evaluate side-chains 317 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 297 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 62 CYS Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 43 TYR Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 785 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 0.9990 chunk 153 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 22 optimal weight: 0.2980 chunk 97 optimal weight: 4.9990 chunk 136 optimal weight: 20.0000 chunk 204 optimal weight: 0.5980 chunk 216 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 193 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 710 GLN J 183 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17462 Z= 0.170 Angle : 0.486 8.617 23698 Z= 0.244 Chirality : 0.039 0.253 2738 Planarity : 0.004 0.040 2886 Dihedral : 9.945 88.459 2964 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.21 % Allowed : 14.36 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: 0.93 (0.18), residues: 2254 helix: 1.98 (0.15), residues: 1312 sheet: -0.48 (0.47), residues: 120 loop : -1.55 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 766 HIS 0.004 0.001 HIS J 105 PHE 0.014 0.001 PHE E 146 TYR 0.013 0.001 TYR D 405 ARG 0.006 0.001 ARG A 657 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 303 time to evaluate : 1.944 Fit side-chains revert: symmetry clash REVERT: A 475 LEU cc_start: 0.7837 (tt) cc_final: 0.7591 (tp) REVERT: A 498 ILE cc_start: 0.8024 (mt) cc_final: 0.7772 (mt) REVERT: A 629 ILE cc_start: 0.5383 (OUTLIER) cc_final: 0.5006 (mm) REVERT: A 747 LEU cc_start: 0.9088 (mm) cc_final: 0.8829 (mt) REVERT: B 585 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8257 (mtp) REVERT: B 714 GLN cc_start: 0.8366 (mm110) cc_final: 0.8124 (mm-40) REVERT: G 35 ARG cc_start: 0.7875 (ttp-170) cc_final: 0.7401 (ttp-170) REVERT: J 26 ILE cc_start: 0.8628 (mm) cc_final: 0.8188 (mt) REVERT: J 43 TYR cc_start: 0.7283 (OUTLIER) cc_final: 0.6405 (t80) REVERT: D 585 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8291 (mtp) outliers start: 33 outliers final: 22 residues processed: 317 average time/residue: 0.3084 time to fit residues: 143.2061 Evaluate side-chains 319 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 293 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain B residue 585 MET Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 90 CYS Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain C residue 754 VAL Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 43 TYR Chi-restraints excluded: chain J residue 90 CYS Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain D residue 585 MET Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 chunk 89 optimal weight: 0.0030 chunk 184 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 110 optimal weight: 0.9980 chunk 194 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 GLN ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 GLN J 183 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17462 Z= 0.225 Angle : 0.497 8.568 23698 Z= 0.250 Chirality : 0.039 0.163 2738 Planarity : 0.003 0.039 2886 Dihedral : 9.737 89.824 2964 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.82 % Allowed : 14.77 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.18), residues: 2254 helix: 1.91 (0.15), residues: 1314 sheet: -0.50 (0.48), residues: 120 loop : -1.47 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 766 HIS 0.004 0.001 HIS I 105 PHE 0.014 0.001 PHE E 146 TYR 0.022 0.001 TYR D 405 ARG 0.007 0.000 ARG A 657 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 306 time to evaluate : 1.879 Fit side-chains revert: symmetry clash REVERT: A 498 ILE cc_start: 0.8043 (mt) cc_final: 0.7784 (mt) REVERT: A 629 ILE cc_start: 0.5406 (OUTLIER) cc_final: 0.5071 (mm) REVERT: A 687 ILE cc_start: 0.7736 (mm) cc_final: 0.7467 (tp) REVERT: B 585 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8357 (mtp) REVERT: B 714 GLN cc_start: 0.8400 (mm110) cc_final: 0.7990 (mm-40) REVERT: G 35 ARG cc_start: 0.7883 (ttp-170) cc_final: 0.7376 (ttp-170) REVERT: I 43 TYR cc_start: 0.7263 (OUTLIER) cc_final: 0.6576 (t80) REVERT: C 629 ILE cc_start: 0.5824 (OUTLIER) cc_final: 0.5438 (mm) REVERT: C 687 ILE cc_start: 0.7669 (mm) cc_final: 0.7467 (tp) REVERT: C 711 ARG cc_start: 0.7081 (mmp80) cc_final: 0.6836 (mmp-170) REVERT: J 26 ILE cc_start: 0.8655 (mm) cc_final: 0.8201 (mt) REVERT: J 43 TYR cc_start: 0.7303 (OUTLIER) cc_final: 0.6379 (t80) REVERT: D 585 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8423 (mtp) REVERT: D 728 ASP cc_start: 0.8098 (p0) cc_final: 0.7834 (p0) outliers start: 42 outliers final: 29 residues processed: 327 average time/residue: 0.3181 time to fit residues: 152.6843 Evaluate side-chains 326 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 291 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 585 MET Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 43 TYR Chi-restraints excluded: chain I residue 90 CYS Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 487 PHE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 62 CYS Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 43 TYR Chi-restraints excluded: chain J residue 90 CYS Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 585 MET Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 736 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 3.9990 chunk 194 optimal weight: 0.0670 chunk 42 optimal weight: 20.0000 chunk 127 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 216 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 100 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 GLN G 107 HIS C 710 GLN J 183 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17462 Z= 0.260 Angle : 0.510 7.273 23698 Z= 0.257 Chirality : 0.040 0.266 2738 Planarity : 0.004 0.040 2886 Dihedral : 9.741 89.907 2964 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.29 % Allowed : 15.44 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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 (0.18), residues: 2254 helix: 1.77 (0.15), residues: 1330 sheet: -0.96 (0.43), residues: 152 loop : -1.49 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 766 HIS 0.003 0.001 HIS E 75 PHE 0.013 0.001 PHE E 146 TYR 0.021 0.001 TYR D 405 ARG 0.009 0.001 ARG C 657 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 293 time to evaluate : 1.741 Fit side-chains REVERT: A 498 ILE cc_start: 0.8092 (mt) cc_final: 0.7863 (mt) REVERT: A 629 ILE cc_start: 0.5426 (OUTLIER) cc_final: 0.5087 (mm) REVERT: B 435 HIS cc_start: 0.6954 (m90) cc_final: 0.6690 (m90) REVERT: B 585 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8414 (mtp) REVERT: B 714 GLN cc_start: 0.8316 (mm110) cc_final: 0.8062 (mm-40) REVERT: G 35 ARG cc_start: 0.7805 (ttp-170) cc_final: 0.7302 (ttp-170) REVERT: C 629 ILE cc_start: 0.5666 (OUTLIER) cc_final: 0.5341 (mm) REVERT: J 26 ILE cc_start: 0.8667 (mm) cc_final: 0.8206 (mt) REVERT: D 585 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8423 (mtp) REVERT: D 728 ASP cc_start: 0.8105 (p0) cc_final: 0.7823 (p0) outliers start: 49 outliers final: 36 residues processed: 322 average time/residue: 0.3155 time to fit residues: 149.3776 Evaluate side-chains 325 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 285 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 585 MET Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 90 CYS Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 487 PHE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain C residue 754 VAL Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 62 CYS Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 90 CYS Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 585 MET Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 736 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 1.9990 chunk 24 optimal weight: 20.0000 chunk 123 optimal weight: 0.9990 chunk 158 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 135 optimal weight: 9.9990 chunk 131 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 GLN I 183 ASN C 710 GLN J 183 ASN D 619 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17462 Z= 0.364 Angle : 0.561 8.284 23698 Z= 0.282 Chirality : 0.042 0.288 2738 Planarity : 0.004 0.042 2886 Dihedral : 9.951 88.583 2964 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.56 % Allowed : 16.24 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: 0.55 (0.18), residues: 2254 helix: 1.62 (0.15), residues: 1326 sheet: -1.21 (0.42), residues: 152 loop : -1.53 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 766 HIS 0.004 0.001 HIS I 105 PHE 0.032 0.002 PHE E 78 TYR 0.023 0.001 TYR D 405 ARG 0.009 0.001 ARG A 657 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 294 time to evaluate : 1.862 Fit side-chains REVERT: A 498 ILE cc_start: 0.8176 (mt) cc_final: 0.7939 (mt) REVERT: A 629 ILE cc_start: 0.5533 (OUTLIER) cc_final: 0.5198 (mm) REVERT: A 711 ARG cc_start: 0.7482 (mmp80) cc_final: 0.7123 (mmp80) REVERT: B 435 HIS cc_start: 0.6922 (m90) cc_final: 0.6692 (m90) REVERT: B 585 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8552 (mtp) REVERT: B 714 GLN cc_start: 0.8371 (mm110) cc_final: 0.8104 (mm-40) REVERT: G 35 ARG cc_start: 0.7884 (ttp-170) cc_final: 0.7318 (ttp-170) REVERT: C 629 ILE cc_start: 0.5845 (OUTLIER) cc_final: 0.5509 (mm) REVERT: J 26 ILE cc_start: 0.8692 (mm) cc_final: 0.8221 (mt) REVERT: D 585 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.8497 (mtp) REVERT: D 728 ASP cc_start: 0.8135 (p0) cc_final: 0.7859 (p0) outliers start: 53 outliers final: 40 residues processed: 324 average time/residue: 0.3086 time to fit residues: 146.9787 Evaluate side-chains 332 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 288 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 585 MET Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 90 CYS Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 487 PHE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 754 VAL Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 31 PHE Chi-restraints excluded: chain E residue 62 CYS Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 90 CYS Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain D residue 585 MET Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 736 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 128 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 41 optimal weight: 0.6980 chunk 137 optimal weight: 8.9990 chunk 147 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 169 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17462 Z= 0.187 Angle : 0.512 9.939 23698 Z= 0.253 Chirality : 0.040 0.353 2738 Planarity : 0.004 0.039 2886 Dihedral : 9.426 88.603 2964 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.02 % Allowed : 17.58 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: 0.83 (0.18), residues: 2254 helix: 1.85 (0.15), residues: 1322 sheet: -1.19 (0.41), residues: 156 loop : -1.40 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 766 HIS 0.002 0.001 HIS I 105 PHE 0.027 0.001 PHE E 78 TYR 0.019 0.001 TYR D 405 ARG 0.010 0.001 ARG A 657 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 297 time to evaluate : 1.938 Fit side-chains REVERT: A 498 ILE cc_start: 0.8155 (mt) cc_final: 0.7930 (mt) REVERT: A 629 ILE cc_start: 0.5669 (OUTLIER) cc_final: 0.5376 (mm) REVERT: B 435 HIS cc_start: 0.6980 (m90) cc_final: 0.6738 (m90) REVERT: B 585 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8438 (mtp) REVERT: B 714 GLN cc_start: 0.8325 (mm110) cc_final: 0.8083 (mm-40) REVERT: B 728 ASP cc_start: 0.8055 (p0) cc_final: 0.7850 (p0) REVERT: G 35 ARG cc_start: 0.7867 (ttp-170) cc_final: 0.7344 (ttp-170) REVERT: C 629 ILE cc_start: 0.5744 (OUTLIER) cc_final: 0.5424 (mm) REVERT: J 26 ILE cc_start: 0.8579 (mm) cc_final: 0.8114 (mt) REVERT: D 585 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8406 (mtp) outliers start: 45 outliers final: 31 residues processed: 321 average time/residue: 0.3120 time to fit residues: 146.7369 Evaluate side-chains 325 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 290 time to evaluate : 1.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 585 MET Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 90 CYS Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 487 PHE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 754 VAL Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 31 PHE Chi-restraints excluded: chain E residue 62 CYS Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 90 CYS Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain D residue 585 MET Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 736 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 0.8980 chunk 206 optimal weight: 5.9990 chunk 188 optimal weight: 0.9980 chunk 201 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 157 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 181 optimal weight: 0.3980 chunk 190 optimal weight: 7.9990 chunk 200 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 183 ASN C 710 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17462 Z= 0.198 Angle : 0.518 11.693 23698 Z= 0.254 Chirality : 0.039 0.334 2738 Planarity : 0.003 0.037 2886 Dihedral : 9.131 88.090 2964 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.82 % Allowed : 18.59 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: 0.88 (0.18), residues: 2254 helix: 1.88 (0.15), residues: 1322 sheet: -1.24 (0.41), residues: 156 loop : -1.34 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 766 HIS 0.003 0.001 HIS I 105 PHE 0.028 0.001 PHE E 78 TYR 0.019 0.001 TYR D 405 ARG 0.009 0.001 ARG A 657 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 294 time to evaluate : 1.780 Fit side-chains REVERT: A 498 ILE cc_start: 0.8183 (mt) cc_final: 0.7948 (mt) REVERT: A 629 ILE cc_start: 0.5626 (OUTLIER) cc_final: 0.5347 (mm) REVERT: B 435 HIS cc_start: 0.6913 (m90) cc_final: 0.6669 (m90) REVERT: B 585 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8480 (mtp) REVERT: B 714 GLN cc_start: 0.8334 (mm110) cc_final: 0.8106 (mm-40) REVERT: B 728 ASP cc_start: 0.8081 (p0) cc_final: 0.7874 (p0) REVERT: G 31 PHE cc_start: 0.7651 (OUTLIER) cc_final: 0.7451 (m-10) REVERT: G 35 ARG cc_start: 0.7852 (ttp-170) cc_final: 0.7328 (ttp-170) REVERT: I 138 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8543 (mp) REVERT: C 629 ILE cc_start: 0.5692 (OUTLIER) cc_final: 0.5367 (mm) REVERT: J 26 ILE cc_start: 0.8579 (mm) cc_final: 0.8116 (mt) REVERT: D 585 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8420 (mtp) outliers start: 42 outliers final: 33 residues processed: 316 average time/residue: 0.3132 time to fit residues: 143.8373 Evaluate side-chains 328 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 289 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 585 MET Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain G residue 31 PHE Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 90 CYS Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 487 PHE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 754 VAL Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 31 PHE Chi-restraints excluded: chain E residue 62 CYS Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 90 CYS Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain D residue 585 MET Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 736 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 0.8980 chunk 212 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 chunk 100 optimal weight: 8.9990 chunk 147 optimal weight: 2.9990 chunk 223 optimal weight: 0.7980 chunk 205 optimal weight: 0.0770 chunk 177 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 137 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 GLN ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 183 ASN C 710 GLN J 183 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17462 Z= 0.190 Angle : 0.516 12.299 23698 Z= 0.254 Chirality : 0.039 0.320 2738 Planarity : 0.004 0.053 2886 Dihedral : 8.930 87.560 2964 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.55 % Allowed : 19.40 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.18), residues: 2254 helix: 1.95 (0.15), residues: 1320 sheet: -1.27 (0.43), residues: 144 loop : -1.19 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 460 HIS 0.004 0.001 HIS I 105 PHE 0.027 0.001 PHE E 78 TYR 0.015 0.001 TYR D 405 ARG 0.008 0.001 ARG A 657 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 294 time to evaluate : 1.701 Fit side-chains REVERT: A 498 ILE cc_start: 0.8143 (mt) cc_final: 0.7852 (mt) REVERT: A 629 ILE cc_start: 0.5627 (OUTLIER) cc_final: 0.5368 (mm) REVERT: B 435 HIS cc_start: 0.6898 (m90) cc_final: 0.6652 (m90) REVERT: B 585 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8416 (mtp) REVERT: B 714 GLN cc_start: 0.8343 (mm110) cc_final: 0.8107 (mm-40) REVERT: B 728 ASP cc_start: 0.8043 (p0) cc_final: 0.7830 (p0) REVERT: G 35 ARG cc_start: 0.7850 (ttp-170) cc_final: 0.7323 (ttp-170) REVERT: I 138 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8536 (mp) REVERT: C 629 ILE cc_start: 0.5499 (OUTLIER) cc_final: 0.5201 (mm) REVERT: J 26 ILE cc_start: 0.8566 (mm) cc_final: 0.8105 (mt) REVERT: D 404 PRO cc_start: 0.7759 (Cg_endo) cc_final: 0.7498 (Cg_exo) REVERT: D 585 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8419 (mtp) REVERT: D 714 GLN cc_start: 0.8437 (mm110) cc_final: 0.8160 (mm110) outliers start: 38 outliers final: 30 residues processed: 317 average time/residue: 0.3253 time to fit residues: 151.2992 Evaluate side-chains 322 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 287 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 585 MET Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 90 CYS Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 487 PHE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 754 VAL Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 62 CYS Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 90 CYS Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain D residue 585 MET Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 736 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 10.0000 chunk 189 optimal weight: 20.0000 chunk 54 optimal weight: 0.7980 chunk 163 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 177 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 182 optimal weight: 1.9990 chunk 22 optimal weight: 0.0470 chunk 32 optimal weight: 5.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 183 ASN C 710 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.170771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.105591 restraints weight = 22022.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.106492 restraints weight = 17556.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.106320 restraints weight = 16395.384| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17462 Z= 0.173 Angle : 0.522 12.288 23698 Z= 0.256 Chirality : 0.039 0.326 2738 Planarity : 0.004 0.050 2886 Dihedral : 8.668 87.197 2964 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.82 % Allowed : 19.26 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: 1.09 (0.18), residues: 2254 helix: 1.99 (0.15), residues: 1320 sheet: -1.26 (0.43), residues: 144 loop : -1.12 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 766 HIS 0.002 0.001 HIS J 105 PHE 0.027 0.001 PHE E 78 TYR 0.017 0.001 TYR B 405 ARG 0.008 0.001 ARG A 657 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3601.09 seconds wall clock time: 66 minutes 0.82 seconds (3960.82 seconds total)