Starting phenix.real_space_refine on Sat Mar 16 03:58:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ocd_12804/03_2024/7ocd_12804_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ocd_12804/03_2024/7ocd_12804.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ocd_12804/03_2024/7ocd_12804_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ocd_12804/03_2024/7ocd_12804_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ocd_12804/03_2024/7ocd_12804_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ocd_12804/03_2024/7ocd_12804.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ocd_12804/03_2024/7ocd_12804.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ocd_12804/03_2024/7ocd_12804_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ocd_12804/03_2024/7ocd_12804_updated.pdb" } resolution = 3.5 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 82 5.16 5 C 8982 2.51 5 N 2194 2.21 5 O 2366 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 515": "OD1" <-> "OD2" Residue "A ARG 541": "NH1" <-> "NH2" Residue "A PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 566": "OE1" <-> "OE2" Residue "A PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 624": "NH1" <-> "NH2" Residue "A GLU 633": "OE1" <-> "OE2" Residue "A TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 706": "OE1" <-> "OE2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 756": "OD1" <-> "OD2" Residue "A TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 515": "OD1" <-> "OD2" Residue "C ARG 541": "NH1" <-> "NH2" Residue "C PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 586": "OD1" <-> "OD2" Residue "C PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 624": "NH1" <-> "NH2" Residue "C GLU 633": "OE1" <-> "OE2" Residue "C TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 756": "OD1" <-> "OD2" Residue "C PHE 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 590": "OD1" <-> "OD2" Residue "D TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 628": "NH1" <-> "NH2" Residue "D TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 710": "OE1" <-> "OE2" Residue "D TYR 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 590": "OD1" <-> "OD2" Residue "B TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "B TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 710": "OE1" <-> "OE2" Residue "B TYR 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13624 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2773 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 381} Chain breaks: 2 Unresolved non-hydrogen bonds: 332 Unresolved non-hydrogen angles: 400 Unresolved non-hydrogen dihedrals: 271 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 22, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 203 Chain: "C" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2773 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 381} Chain breaks: 2 Unresolved non-hydrogen bonds: 332 Unresolved non-hydrogen angles: 400 Unresolved non-hydrogen dihedrals: 271 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 22, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 203 Chain: "D" Number of atoms: 2777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2777 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 382} Chain breaks: 2 Unresolved non-hydrogen bonds: 326 Unresolved non-hydrogen angles: 381 Unresolved non-hydrogen dihedrals: 275 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 13, 'PHE:plan': 1, 'GLU:plan': 21, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 180 Chain: "I" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1153 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 1, 'TRANS': 167} Chain breaks: 3 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 87 Chain: "J" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1153 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 1, 'TRANS': 167} Chain breaks: 3 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 87 Chain: "B" Number of atoms: 2777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2777 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 382} Chain breaks: 2 Unresolved non-hydrogen bonds: 326 Unresolved non-hydrogen angles: 381 Unresolved non-hydrogen dihedrals: 275 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 13, 'PHE:plan': 1, 'GLU:plan': 21, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 180 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {'E2Q': 1, 'PC1': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 66 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {'E2Q': 1, 'PC1': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 66 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: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'E2Q': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'E2Q': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 7.51, per 1000 atoms: 0.55 Number of scatterers: 13624 At special positions: 0 Unit cell: (129.47, 110.21, 131.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 82 16.00 O 2366 8.00 N 2194 7.00 C 8982 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 C 714 " - pdb=" SG CYS C 769 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS I 52 " - pdb=" SG CYS I 91 " distance=2.03 Simple disulfide: pdb=" SG CYS I 90 " - pdb=" SG CYS I 100 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 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: 5.75 Conformation dependent library (CDL) restraints added in 2.6 seconds 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3496 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 76 helices and 12 sheets defined 51.0% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.70 Creating SS restraints... Processing helix chain 'A' and resid 408 through 410 No H-bonds generated for 'chain 'A' and resid 408 through 410' Processing helix chain 'A' and resid 413 through 416 Processing helix chain 'A' and resid 420 through 432 Processing helix chain 'A' and resid 459 through 464 Processing helix chain 'A' and resid 479 through 484 removed outlier: 3.655A pdb=" N VAL A 484 " --> pdb=" O VAL A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 514 No H-bonds generated for 'chain 'A' and resid 512 through 514' Processing helix chain 'A' and resid 519 through 541 Processing helix chain 'A' and resid 569 through 580 Processing helix chain 'A' and resid 592 through 622 Processing helix chain 'A' and resid 632 through 637 Processing helix chain 'A' and resid 650 through 656 Processing helix chain 'A' and resid 661 through 671 Processing helix chain 'A' and resid 682 through 691 Processing helix chain 'A' and resid 702 through 710 removed outlier: 3.519A pdb=" N GLN A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 751 Processing helix chain 'A' and resid 755 through 763 Processing helix chain 'A' and resid 785 through 787 No H-bonds generated for 'chain 'A' and resid 785 through 787' Processing helix chain 'A' and resid 789 through 814 removed outlier: 3.545A pdb=" N SER A 814 " --> pdb=" O PHE A 810 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 410 No H-bonds generated for 'chain 'C' and resid 408 through 410' Processing helix chain 'C' and resid 413 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 484 removed outlier: 3.652A pdb=" N VAL C 484 " --> pdb=" O VAL C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 514 No H-bonds generated for 'chain 'C' and resid 512 through 514' Processing helix chain 'C' and resid 519 through 541 Processing helix chain 'C' and resid 569 through 580 Processing helix chain 'C' and resid 592 through 622 Processing helix chain 'C' and resid 632 through 637 Processing helix chain 'C' and resid 650 through 656 Processing helix chain 'C' and resid 661 through 671 Processing helix chain 'C' and resid 682 through 692 Processing helix chain 'C' and resid 702 through 710 Processing helix chain 'C' and resid 739 through 751 Processing helix chain 'C' and resid 755 through 763 Processing helix chain 'C' and resid 785 through 787 No H-bonds generated for 'chain 'C' and resid 785 through 787' Processing helix chain 'C' and resid 789 through 814 removed outlier: 3.544A pdb=" N SER C 814 " --> pdb=" O PHE C 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 436 removed outlier: 3.584A pdb=" N HIS D 435 " --> pdb=" O GLU D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 468 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 516 through 518 No H-bonds generated for 'chain 'D' and resid 516 through 518' Processing helix chain 'D' and resid 523 through 546 Processing helix chain 'D' and resid 573 through 584 Processing helix chain 'D' and resid 596 through 625 Processing helix chain 'D' and resid 636 through 640 Processing helix chain 'D' and resid 654 through 660 Processing helix chain 'D' and resid 665 through 675 removed outlier: 3.531A pdb=" N MET D 670 " --> pdb=" O VAL D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 695 Processing helix chain 'D' and resid 706 through 714 removed outlier: 3.600A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 743 through 756 Processing helix chain 'D' and resid 759 through 767 Processing helix chain 'D' and resid 789 through 818 removed outlier: 5.685A pdb=" N GLY D 794 " --> pdb=" O SER D 790 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL D 795 " --> pdb=" O ASN D 791 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 40 Processing helix chain 'I' and resid 118 through 126 Processing helix chain 'I' and resid 129 through 149 Processing helix chain 'I' and resid 157 through 183 Processing helix chain 'I' and resid 203 through 230 Processing helix chain 'J' and resid 20 through 40 Processing helix chain 'J' and resid 118 through 126 Processing helix chain 'J' and resid 129 through 149 Processing helix chain 'J' and resid 157 through 183 Processing helix chain 'J' and resid 203 through 230 Processing helix chain 'B' and resid 424 through 436 removed outlier: 3.584A pdb=" N HIS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 468 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 516 through 518 No H-bonds generated for 'chain 'B' and resid 516 through 518' Processing helix chain 'B' and resid 523 through 546 Processing helix chain 'B' and resid 573 through 584 Processing helix chain 'B' and resid 596 through 625 Processing helix chain 'B' and resid 636 through 640 Processing helix chain 'B' and resid 654 through 660 Processing helix chain 'B' and resid 665 through 675 removed outlier: 3.531A pdb=" N MET B 670 " --> pdb=" O VAL B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 695 Processing helix chain 'B' and resid 706 through 714 removed outlier: 3.599A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 756 Processing helix chain 'B' and resid 759 through 767 Processing helix chain 'B' and resid 789 through 818 removed outlier: 5.685A pdb=" N GLY B 794 " --> pdb=" O SER B 790 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL B 795 " --> pdb=" O ASN B 791 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 392 through 395 removed outlier: 6.427A pdb=" N ARG A 437 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N THR A 395 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLU A 439 " --> pdb=" O THR A 395 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 492 through 494 removed outlier: 3.673A pdb=" N MET A 492 " --> pdb=" O TYR A 728 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 494 " --> pdb=" O LYS A 726 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 716 through 719 removed outlier: 4.286A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 700 " --> pdb=" O SER A 497 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS A 501 " --> pdb=" O TYR A 696 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N TYR A 696 " --> pdb=" O LYS A 501 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ALA A 642 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N LEU A 699 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLY A 644 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 9.142A pdb=" N GLU A 701 " --> pdb=" O GLY A 644 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 392 through 395 removed outlier: 6.437A pdb=" N ARG C 437 " --> pdb=" O VAL C 393 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N THR C 395 " --> pdb=" O ARG C 437 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLU C 439 " --> pdb=" O THR C 395 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 492 through 494 removed outlier: 3.692A pdb=" N MET C 492 " --> pdb=" O TYR C 728 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU C 494 " --> pdb=" O LYS C 726 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 716 through 719 removed outlier: 4.279A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU C 700 " --> pdb=" O SER C 497 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LYS C 501 " --> pdb=" O TYR C 696 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N TYR C 696 " --> pdb=" O LYS C 501 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 9.148A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.653A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 720 through 723 removed outlier: 3.732A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU D 704 " --> pdb=" O SER D 501 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 10.020A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'I' and resid 80 through 84 Processing sheet with id= J, first strand: chain 'J' and resid 80 through 84 Processing sheet with id= K, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.653A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 720 through 723 removed outlier: 3.732A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B 704 " --> pdb=" O SER B 501 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 10.021A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) 718 hydrogen bonds defined for protein. 2124 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: 4.11 Time building geometry restraints manager: 6.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2056 1.31 - 1.43: 3969 1.43 - 1.56: 7773 1.56 - 1.68: 4 1.68 - 1.81: 126 Bond restraints: 13928 Sorted by residual: bond pdb=" N15 E2Q A 901 " pdb=" O17 E2Q A 901 " ideal model delta sigma weight residual 1.401 1.186 0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" N15 E2Q C 901 " pdb=" O17 E2Q C 901 " ideal model delta sigma weight residual 1.401 1.187 0.214 2.00e-02 2.50e+03 1.15e+02 bond pdb=" N15 E2Q D 901 " pdb=" O17 E2Q D 901 " ideal model delta sigma weight residual 1.401 1.188 0.213 2.00e-02 2.50e+03 1.14e+02 bond pdb=" N15 E2Q B 901 " pdb=" O17 E2Q B 901 " ideal model delta sigma weight residual 1.401 1.189 0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C09 E2Q A 901 " pdb=" S11 E2Q A 901 " ideal model delta sigma weight residual 1.820 1.691 0.129 2.00e-02 2.50e+03 4.15e+01 ... (remaining 13923 not shown) Histogram of bond angle deviations from ideal: 96.92 - 104.35: 164 104.35 - 111.78: 7097 111.78 - 119.20: 3922 119.20 - 126.63: 7648 126.63 - 134.06: 199 Bond angle restraints: 19030 Sorted by residual: angle pdb=" O12 E2Q A 901 " pdb=" S11 E2Q A 901 " pdb=" O13 E2Q A 901 " ideal model delta sigma weight residual 101.20 123.42 -22.22 3.00e+00 1.11e-01 5.49e+01 angle pdb=" O12 E2Q C 901 " pdb=" S11 E2Q C 901 " pdb=" O13 E2Q C 901 " ideal model delta sigma weight residual 101.20 123.32 -22.12 3.00e+00 1.11e-01 5.44e+01 angle pdb=" O12 E2Q D 901 " pdb=" S11 E2Q D 901 " pdb=" O13 E2Q D 901 " ideal model delta sigma weight residual 101.20 123.01 -21.81 3.00e+00 1.11e-01 5.29e+01 angle pdb=" O12 E2Q B 901 " pdb=" S11 E2Q B 901 " pdb=" O13 E2Q B 901 " ideal model delta sigma weight residual 101.20 123.01 -21.81 3.00e+00 1.11e-01 5.29e+01 angle pdb=" C10 E2Q A 901 " pdb=" C09 E2Q A 901 " pdb=" S11 E2Q A 901 " ideal model delta sigma weight residual 102.48 118.34 -15.86 3.00e+00 1.11e-01 2.79e+01 ... (remaining 19025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.93: 7185 15.93 - 31.85: 564 31.85 - 47.78: 91 47.78 - 63.70: 32 63.70 - 79.63: 8 Dihedral angle restraints: 7880 sinusoidal: 2392 harmonic: 5488 Sorted by residual: dihedral pdb=" CB CYS C 714 " pdb=" SG CYS C 714 " pdb=" SG CYS C 769 " pdb=" CB CYS C 769 " ideal model delta sinusoidal sigma weight residual 93.00 161.07 -68.07 1 1.00e+01 1.00e-02 6.01e+01 dihedral pdb=" CB CYS A 714 " pdb=" SG CYS A 714 " pdb=" SG CYS A 769 " pdb=" CB CYS A 769 " ideal model delta sinusoidal sigma weight residual 93.00 160.30 -67.30 1 1.00e+01 1.00e-02 5.90e+01 dihedral pdb=" CB CYS J 52 " pdb=" SG CYS J 52 " pdb=" SG CYS J 91 " pdb=" CB CYS J 91 " ideal model delta sinusoidal sigma weight residual 93.00 138.96 -45.96 1 1.00e+01 1.00e-02 2.93e+01 ... (remaining 7877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1243 0.027 - 0.055: 619 0.055 - 0.082: 299 0.082 - 0.109: 81 0.109 - 0.137: 28 Chirality restraints: 2270 Sorted by residual: chirality pdb=" CG LEU C 538 " pdb=" CB LEU C 538 " pdb=" CD1 LEU C 538 " pdb=" CD2 LEU C 538 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 4.67e-01 chirality pdb=" CA VAL D 406 " pdb=" N VAL D 406 " pdb=" C VAL D 406 " pdb=" CB VAL D 406 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA VAL B 406 " pdb=" N VAL B 406 " pdb=" C VAL B 406 " pdb=" CB VAL B 406 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.51e-01 ... (remaining 2267 not shown) Planarity restraints: 2320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 515 " 0.024 5.00e-02 4.00e+02 3.60e-02 2.07e+00 pdb=" N PRO A 516 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 516 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 516 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 119 " 0.013 2.00e-02 2.50e+03 8.70e-03 1.51e+00 pdb=" CG TYR I 119 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR I 119 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR I 119 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR I 119 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR I 119 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR I 119 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR I 119 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 119 " -0.013 2.00e-02 2.50e+03 8.66e-03 1.50e+00 pdb=" CG TYR J 119 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR J 119 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR J 119 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR J 119 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR J 119 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR J 119 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR J 119 " -0.009 2.00e-02 2.50e+03 ... (remaining 2317 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 294 2.69 - 3.24: 14382 3.24 - 3.79: 22130 3.79 - 4.35: 26538 4.35 - 4.90: 45610 Nonbonded interactions: 108954 Sorted by model distance: nonbonded pdb=" N14 E2Q A 901 " pdb=" O16 E2Q A 901 " model vdw 2.132 2.520 nonbonded pdb=" N14 E2Q C 901 " pdb=" O16 E2Q C 901 " model vdw 2.135 2.520 nonbonded pdb=" OD2 ASP C 586 " pdb=" OG SER D 592 " model vdw 2.138 2.440 nonbonded pdb=" N14 E2Q B 901 " pdb=" O16 E2Q B 901 " model vdw 2.140 2.520 nonbonded pdb=" N14 E2Q D 901 " pdb=" O16 E2Q D 901 " model vdw 2.140 2.520 ... (remaining 108949 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 398 or resid 400 through 403 or resid 405 thro \ ugh 407 or resid 412 through 414 or resid 416 through 422 or resid 424 through 4 \ 27 or (resid 428 through 430 and (name N or name CA or name C or name O or name \ CB )) or resid 431 or resid 433 or resid 436 or resid 438 or resid 440 or (resid \ 441 and (name N or name CA or name C or name O or name CB )) or resid 443 throu \ gh 450 or resid 452 through 454 or resid 456 through 458 or (resid 459 and (name \ N or name CA or name C or name O or name CB )) or resid 460 through 466 or resi \ d 468 through 469 or resid 471 or resid 473 through 485 or (resid 486 and (name \ N or name CA or name C or name O or name CB )) or resid 487 through 500 or (resi \ d 501 through 502 and (name N or name CA or name C or name O or name CB )) or re \ sid 503 through 514 or (resid 515 and (name N or name CA or name C or name O or \ name CB )) or resid 516 through 519 or (resid 520 and (name N or name CA or name \ C or name O or name CB )) or resid 521 through 540 or (resid 541 and (name N or \ name CA or name C or name O or name CB )) or resid 542 through 543 or (resid 56 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 567 through \ 581 or resid 583 through 632 or (resid 633 through 634 and (name N or name CA or \ name C or name O or name CB )) or resid 635 or resid 637 through 646 or resid 6 \ 49 through 663 or (resid 665 through 666 and (name N or name CA or name C or nam \ e O or name CB )) or resid 667 through 670 or resid 672 through 682 or resid 684 \ through 685 or resid 688 through 736 or resid 738 or resid 741 through 751 or ( \ resid 752 and (name N or name CA or name C or name O or name CB )) or resid 753 \ through 755 or (resid 756 through 757 and (name N or name CA or name C or name O \ or name CB )) or resid 758 through 759 or (resid 761 and (name N or name CA or \ name C or name O or name CB )) or resid 762 through 765 or (resid 766 and (name \ N or name CA or name C or name O or name CB )) or resid 767 through 795 or resid \ 797 through 815 or resid 901)) selection = (chain 'B' and (resid 397 through 402 or resid 404 through 407 or resid 409 thro \ ugh 411 or (resid 416 through 418 and (name N or name CA or name C or name O or \ name CB )) or (resid 420 and (name N or name CA or name C or name O or name CB ) \ ) or resid 421 through 424 or (resid 425 through 426 and (name N or name CA or n \ ame C or name O or name CB )) or resid 428 through 435 or resid 437 or resid 440 \ or resid 442 or resid 444 through 445 or resid 447 through 454 or resid 456 thr \ ough 458 or resid 460 or (resid 461 and (name N or name CA or name C or name O o \ r name CB )) or resid 462 through 470 or resid 472 through 473 or resid 475 or r \ esid 477 through 488 or (resid 489 through 490 and (name N or name CA or name C \ or name O or name CB )) or resid 491 through 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 547 or \ resid 570 through 575 or (resid 576 and (name N or name CA or name C or name O o \ r name CB )) or resid 577 through 585 or resid 587 through 630 or (resid 631 and \ (name N or name CA or name C or name O or name CB )) or resid 632 or (resid 633 \ through 634 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 35 through 639 or resid 641 through 642 or (resid 643 through 644 and (name N or \ name CA or name C or name O or name CB )) or resid 645 through 650 or resid 653 \ or (resid 654 and (name N or name CA or name C or name O or name CB )) or resid \ 655 through 663 or (resid 664 through 666 and (name N or name CA or name C or n \ ame O or name CB )) or resid 667 or resid 669 through 671 or (resid 672 and (nam \ e N or name CA or name C or name O or name CB )) or resid 673 through 674 or res \ id 676 through 684 or (resid 685 and (name N or name CA or name C or name O or n \ ame CB )) or resid 686 or resid 688 through 689 or (resid 692 and (name N or nam \ e CA or name C or name O or name CB )) or resid 693 through 695 or (resid 696 th \ rough 697 and (name N or name CA or name C or name O or name CB )) or resid 698 \ through 714 or (resid 715 through 716 and (name N or name CA or name C or name O \ or name CB )) or resid 717 through 729 or (resid 730 and (name N or name CA or \ name C or name O or name CB or name CG or name CE or name NZ )) or resid 731 thr \ ough 740 or resid 742 or resid 745 through 754 or (resid 755 through 756 and (na \ me N or name CA or name C or name O or name CB )) or resid 757 through 763 or re \ sid 765 through 774 or (resid 784 and (name N or name CA or name C or name O or \ name CB )) or resid 785 through 799 or resid 801 through 817 or (resid 818 throu \ gh 819 and (name N or name CA or name C or name O or name CB )) or resid 901)) selection = (chain 'C' and (resid 393 through 398 or resid 400 through 403 or resid 405 thro \ ugh 407 or resid 412 through 414 or resid 416 through 422 or resid 424 through 4 \ 27 or (resid 428 through 430 and (name N or name CA or name C or name O or name \ CB )) or resid 431 or resid 433 or resid 436 or resid 438 or resid 440 or (resid \ 441 and (name N or name CA or name C or name O or name CB )) or resid 443 throu \ gh 450 or resid 452 through 454 or resid 456 through 458 or (resid 459 and (name \ N or name CA or name C or name O or name CB )) or resid 460 through 466 or resi \ d 468 through 469 or resid 471 or resid 473 through 485 or (resid 486 and (name \ N or name CA or name C or name O or name CB )) or resid 487 through 500 or (resi \ d 501 through 502 and (name N or name CA or name C or name O or name CB )) or re \ sid 503 through 514 or (resid 515 and (name N or name CA or name C or name O or \ name CB )) or resid 516 through 519 or (resid 520 and (name N or name CA or name \ C or name O or name CB )) or resid 521 through 540 or (resid 541 and (name N or \ name CA or name C or name O or name CB )) or resid 542 through 543 or (resid 56 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 567 through \ 581 or resid 583 through 632 or (resid 633 through 634 and (name N or name CA or \ name C or name O or name CB )) or resid 635 or resid 637 through 646 or resid 6 \ 49 through 663 or (resid 665 through 666 and (name N or name CA or name C or nam \ e O or name CB )) or resid 667 through 670 or resid 672 through 682 or resid 684 \ through 685 or resid 688 through 736 or resid 738 or resid 741 through 751 or ( \ resid 752 and (name N or name CA or name C or name O or name CB )) or resid 753 \ through 755 or (resid 756 through 757 and (name N or name CA or name C or name O \ or name CB )) or resid 758 through 759 or (resid 761 and (name N or name CA or \ name C or name O or name CB )) or resid 762 through 765 or (resid 766 and (name \ N or name CA or name C or name O or name CB )) or resid 767 through 795 or resid \ 797 through 815 or resid 901)) selection = (chain 'D' and (resid 397 through 402 or resid 404 through 407 or resid 409 thro \ ugh 411 or (resid 416 through 418 and (name N or name CA or name C or name O or \ name CB )) or (resid 420 and (name N or name CA or name C or name O or name CB ) \ ) or resid 421 through 424 or (resid 425 through 426 and (name N or name CA or n \ ame C or name O or name CB )) or resid 428 through 435 or resid 437 or resid 440 \ or resid 442 or resid 444 through 445 or resid 447 through 454 or resid 456 thr \ ough 458 or resid 460 or (resid 461 and (name N or name CA or name C or name O o \ r name CB )) or resid 462 through 470 or resid 472 through 473 or resid 475 or r \ esid 477 through 488 or (resid 489 through 490 and (name N or name CA or name C \ or name O or name CB )) or resid 491 through 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 547 or \ resid 570 through 575 or (resid 576 and (name N or name CA or name C or name O o \ r name CB )) or resid 577 through 585 or resid 587 through 630 or (resid 631 and \ (name N or name CA or name C or name O or name CB )) or resid 632 or (resid 633 \ through 634 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 35 through 639 or resid 641 through 642 or (resid 643 through 644 and (name N or \ name CA or name C or name O or name CB )) or resid 645 through 650 or resid 653 \ or (resid 654 and (name N or name CA or name C or name O or name CB )) or resid \ 655 through 663 or (resid 664 through 666 and (name N or name CA or name C or n \ ame O or name CB )) or resid 667 or resid 669 through 671 or (resid 672 and (nam \ e N or name CA or name C or name O or name CB )) or resid 673 through 674 or res \ id 676 through 684 or (resid 685 and (name N or name CA or name C or name O or n \ ame CB )) or resid 686 or resid 688 through 689 or (resid 692 and (name N or nam \ e CA or name C or name O or name CB )) or resid 693 through 695 or (resid 696 th \ rough 697 and (name N or name CA or name C or name O or name CB )) or resid 698 \ through 714 or (resid 715 through 716 and (name N or name CA or name C or name O \ or name CB )) or resid 717 through 729 or (resid 730 and (name N or name CA or \ name C or name O or name CB or name CG or name CE or name NZ )) or resid 731 thr \ ough 740 or resid 742 or resid 745 through 754 or (resid 755 through 756 and (na \ me N or name CA or name C or name O or name CB )) or resid 757 through 763 or re \ sid 765 through 774 or (resid 784 and (name N or name CA or name C or name O or \ name CB )) or resid 785 through 799 or resid 801 through 817 or (resid 818 throu \ gh 819 and (name N or name CA or name C or name O or name CB )) or resid 901)) } 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: 2.560 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: 6.710 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 39.560 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 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 : 0.009 0.215 13928 Z= 0.627 Angle : 0.877 22.222 19030 Z= 0.391 Chirality : 0.040 0.137 2270 Planarity : 0.003 0.036 2320 Dihedral : 12.516 79.627 4360 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 0.37 (0.20), residues: 1880 helix: 1.77 (0.16), residues: 1068 sheet: -2.21 (0.44), residues: 146 loop : -1.77 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 767 HIS 0.009 0.003 HIS A 431 PHE 0.011 0.001 PHE C 810 TYR 0.018 0.001 TYR J 119 ARG 0.010 0.001 ARG C 467 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.575 Fit side-chains REVERT: A 701 GLU cc_start: 0.7997 (mp0) cc_final: 0.7683 (mp0) REVERT: C 701 GLU cc_start: 0.8047 (mp0) cc_final: 0.7644 (mp0) REVERT: D 496 MET cc_start: 0.8738 (ttp) cc_final: 0.8535 (ttp) REVERT: D 586 ARG cc_start: 0.8109 (mmm-85) cc_final: 0.7479 (ttp80) REVERT: D 709 ASN cc_start: 0.8197 (t0) cc_final: 0.7797 (t0) REVERT: B 496 MET cc_start: 0.8734 (ttp) cc_final: 0.8534 (ttp) REVERT: B 709 ASN cc_start: 0.8160 (t0) cc_final: 0.7748 (t0) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.2631 time to fit residues: 67.4230 Evaluate side-chains 138 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 0.0000 chunk 142 optimal weight: 20.0000 chunk 79 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13928 Z= 0.164 Angle : 0.483 8.680 19030 Z= 0.244 Chirality : 0.039 0.145 2270 Planarity : 0.003 0.047 2320 Dihedral : 6.310 69.705 2138 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.03 % Allowed : 7.90 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 1.07 (0.21), residues: 1880 helix: 2.30 (0.17), residues: 1070 sheet: -2.24 (0.42), residues: 158 loop : -1.27 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 667 HIS 0.002 0.001 HIS J 83 PHE 0.023 0.001 PHE J 32 TYR 0.011 0.001 TYR C 519 ARG 0.009 0.001 ARG I 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 177 time to evaluate : 1.404 Fit side-chains REVERT: A 395 THR cc_start: 0.8854 (m) cc_final: 0.8617 (m) REVERT: A 701 GLU cc_start: 0.8145 (mp0) cc_final: 0.7695 (mp0) REVERT: D 586 ARG cc_start: 0.7982 (mmm-85) cc_final: 0.7584 (mmm160) REVERT: D 709 ASN cc_start: 0.8415 (t0) cc_final: 0.7754 (t0) REVERT: B 508 GLN cc_start: 0.8146 (mt0) cc_final: 0.7821 (mt0) REVERT: B 709 ASN cc_start: 0.8416 (t0) cc_final: 0.7773 (t0) outliers start: 12 outliers final: 10 residues processed: 184 average time/residue: 0.2844 time to fit residues: 73.5094 Evaluate side-chains 159 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 149 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 HIS Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain D residue 628 ARG Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 628 ARG Chi-restraints excluded: chain B residue 807 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 142 optimal weight: 0.0770 chunk 116 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 171 optimal weight: 0.9980 chunk 184 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 169 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13928 Z= 0.206 Angle : 0.472 9.403 19030 Z= 0.240 Chirality : 0.039 0.133 2270 Planarity : 0.003 0.046 2320 Dihedral : 5.901 70.201 2138 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.55 % Allowed : 12.54 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.21), residues: 1880 helix: 2.24 (0.17), residues: 1072 sheet: -2.05 (0.46), residues: 140 loop : -1.19 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 578 HIS 0.001 0.000 HIS I 83 PHE 0.022 0.001 PHE J 207 TYR 0.014 0.001 TYR C 669 ARG 0.009 0.001 ARG I 97 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 168 time to evaluate : 1.558 Fit side-chains REVERT: A 395 THR cc_start: 0.9101 (OUTLIER) cc_final: 0.8884 (m) REVERT: A 541 ARG cc_start: 0.8123 (tpp80) cc_final: 0.7373 (tpp80) REVERT: A 701 GLU cc_start: 0.8220 (mp0) cc_final: 0.7586 (mp0) REVERT: C 541 ARG cc_start: 0.8080 (tpp80) cc_final: 0.7288 (tpp80) REVERT: D 586 ARG cc_start: 0.8064 (mmm-85) cc_final: 0.7467 (mmm160) REVERT: J 145 VAL cc_start: 0.7470 (p) cc_final: 0.7146 (m) outliers start: 18 outliers final: 11 residues processed: 173 average time/residue: 0.2884 time to fit residues: 70.9574 Evaluate side-chains 162 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 150 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 431 HIS Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain I residue 183 ASN Chi-restraints excluded: chain J residue 183 ASN Chi-restraints excluded: chain J residue 218 ILE Chi-restraints excluded: chain B residue 807 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 0.7980 chunk 128 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 18 optimal weight: 0.3980 chunk 81 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 171 optimal weight: 8.9990 chunk 181 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 162 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 508 GLN ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13928 Z= 0.227 Angle : 0.479 9.811 19030 Z= 0.244 Chirality : 0.039 0.133 2270 Planarity : 0.003 0.043 2320 Dihedral : 5.909 71.450 2138 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.06 % Allowed : 15.55 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 1.08 (0.21), residues: 1880 helix: 2.21 (0.17), residues: 1070 sheet: -1.94 (0.47), residues: 134 loop : -1.22 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 578 HIS 0.003 0.001 HIS J 83 PHE 0.013 0.001 PHE I 32 TYR 0.015 0.001 TYR I 119 ARG 0.011 0.001 ARG I 97 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 156 time to evaluate : 1.525 Fit side-chains REVERT: A 395 THR cc_start: 0.9103 (OUTLIER) cc_final: 0.8894 (m) REVERT: A 541 ARG cc_start: 0.8086 (tpp80) cc_final: 0.7596 (tpp80) REVERT: A 701 GLU cc_start: 0.8264 (mp0) cc_final: 0.7835 (mp0) REVERT: C 541 ARG cc_start: 0.8100 (tpp80) cc_final: 0.7536 (tpp80) REVERT: C 701 GLU cc_start: 0.8323 (mp0) cc_final: 0.8048 (mp0) REVERT: D 586 ARG cc_start: 0.8110 (mmm-85) cc_final: 0.7591 (mmm160) REVERT: J 145 VAL cc_start: 0.7493 (p) cc_final: 0.7188 (m) outliers start: 24 outliers final: 16 residues processed: 170 average time/residue: 0.2846 time to fit residues: 68.8233 Evaluate side-chains 163 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 146 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 431 HIS Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 183 ASN Chi-restraints excluded: chain J residue 183 ASN Chi-restraints excluded: chain J residue 218 ILE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 755 GLU Chi-restraints excluded: chain B residue 807 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 135 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 163 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 508 GLN ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.072 13928 Z= 0.645 Angle : 0.708 11.177 19030 Z= 0.364 Chirality : 0.045 0.159 2270 Planarity : 0.004 0.046 2320 Dihedral : 7.094 82.882 2138 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.18 % Allowed : 17.53 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 0.28 (0.20), residues: 1880 helix: 1.53 (0.16), residues: 1054 sheet: -2.25 (0.44), residues: 142 loop : -1.42 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 578 HIS 0.003 0.001 HIS J 83 PHE 0.018 0.002 PHE D 495 TYR 0.016 0.002 TYR D 424 ARG 0.010 0.001 ARG I 97 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 143 time to evaluate : 1.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 395 THR cc_start: 0.9285 (OUTLIER) cc_final: 0.9071 (m) REVERT: C 701 GLU cc_start: 0.8285 (mp0) cc_final: 0.8003 (mp0) REVERT: D 586 ARG cc_start: 0.8311 (mmm-85) cc_final: 0.7708 (mmm160) REVERT: B 400 ILE cc_start: 0.7149 (mp) cc_final: 0.6891 (tt) outliers start: 37 outliers final: 21 residues processed: 166 average time/residue: 0.2849 time to fit residues: 67.1781 Evaluate side-chains 159 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 137 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain D residue 816 TYR Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 183 ASN Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 183 ASN Chi-restraints excluded: chain J residue 218 ILE Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 755 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 4.9990 chunk 163 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 181 optimal weight: 0.9990 chunk 150 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 508 GLN ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13928 Z= 0.196 Angle : 0.490 11.362 19030 Z= 0.248 Chirality : 0.039 0.121 2270 Planarity : 0.004 0.055 2320 Dihedral : 6.388 83.986 2138 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.23 % Allowed : 20.10 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 0.80 (0.21), residues: 1880 helix: 1.98 (0.17), residues: 1074 sheet: -2.11 (0.47), residues: 134 loop : -1.34 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 767 HIS 0.003 0.001 HIS I 83 PHE 0.017 0.001 PHE I 165 TYR 0.017 0.001 TYR A 669 ARG 0.012 0.001 ARG I 97 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 161 time to evaluate : 1.620 Fit side-chains REVERT: A 395 THR cc_start: 0.9195 (OUTLIER) cc_final: 0.8944 (m) REVERT: A 701 GLU cc_start: 0.8285 (mp0) cc_final: 0.8018 (mp0) REVERT: C 395 THR cc_start: 0.9029 (m) cc_final: 0.8800 (m) REVERT: C 541 ARG cc_start: 0.8018 (tpp80) cc_final: 0.7771 (tpp80) REVERT: C 701 GLU cc_start: 0.8268 (mp0) cc_final: 0.7982 (mp0) REVERT: D 586 ARG cc_start: 0.8182 (mmm-85) cc_final: 0.7697 (mmm160) REVERT: D 755 GLU cc_start: 0.7888 (pt0) cc_final: 0.7651 (mt-10) REVERT: I 207 PHE cc_start: 0.8986 (m-80) cc_final: 0.8766 (m-80) REVERT: J 145 VAL cc_start: 0.7429 (p) cc_final: 0.7226 (m) REVERT: B 755 GLU cc_start: 0.7884 (pt0) cc_final: 0.7616 (mt-10) outliers start: 26 outliers final: 15 residues processed: 177 average time/residue: 0.2831 time to fit residues: 71.4459 Evaluate side-chains 172 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 156 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain I residue 183 ASN Chi-restraints excluded: chain J residue 183 ASN Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 789 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 132 optimal weight: 0.5980 chunk 102 optimal weight: 0.7980 chunk 153 optimal weight: 0.1980 chunk 101 optimal weight: 0.8980 chunk 181 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 110 optimal weight: 0.0970 chunk 83 optimal weight: 8.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 508 GLN ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13928 Z= 0.149 Angle : 0.473 11.501 19030 Z= 0.235 Chirality : 0.038 0.133 2270 Planarity : 0.004 0.056 2320 Dihedral : 6.042 84.250 2138 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.98 % Allowed : 20.53 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 1.12 (0.21), residues: 1880 helix: 2.24 (0.17), residues: 1070 sheet: -2.10 (0.47), residues: 134 loop : -1.15 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 767 HIS 0.002 0.001 HIS I 83 PHE 0.012 0.001 PHE I 207 TYR 0.017 0.001 TYR C 669 ARG 0.014 0.001 ARG I 97 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 168 time to evaluate : 1.678 Fit side-chains REVERT: A 395 THR cc_start: 0.9193 (OUTLIER) cc_final: 0.8950 (m) REVERT: A 701 GLU cc_start: 0.8239 (mp0) cc_final: 0.7973 (mp0) REVERT: C 395 THR cc_start: 0.8950 (m) cc_final: 0.8692 (m) REVERT: C 701 GLU cc_start: 0.8198 (mp0) cc_final: 0.7902 (mp0) REVERT: D 586 ARG cc_start: 0.8100 (mmm-85) cc_final: 0.7549 (mmm160) REVERT: I 207 PHE cc_start: 0.9000 (m-80) cc_final: 0.8768 (m-80) REVERT: J 145 VAL cc_start: 0.7432 (p) cc_final: 0.7228 (m) outliers start: 23 outliers final: 13 residues processed: 185 average time/residue: 0.2694 time to fit residues: 72.2498 Evaluate side-chains 174 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 160 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain I residue 183 ASN Chi-restraints excluded: chain J residue 183 ASN Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 789 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 35 optimal weight: 0.2980 chunk 115 optimal weight: 0.5980 chunk 123 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 chunk 164 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 508 GLN ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13928 Z= 0.229 Angle : 0.508 11.596 19030 Z= 0.254 Chirality : 0.038 0.145 2270 Planarity : 0.004 0.059 2320 Dihedral : 6.158 86.771 2138 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.55 % Allowed : 20.10 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.21), residues: 1880 helix: 2.24 (0.17), residues: 1068 sheet: -2.14 (0.47), residues: 134 loop : -1.11 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 574 HIS 0.002 0.001 HIS I 105 PHE 0.011 0.001 PHE I 207 TYR 0.015 0.001 TYR A 669 ARG 0.015 0.001 ARG I 97 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 154 time to evaluate : 1.650 Fit side-chains REVERT: A 395 THR cc_start: 0.9207 (OUTLIER) cc_final: 0.8969 (m) REVERT: A 701 GLU cc_start: 0.8274 (mp0) cc_final: 0.7976 (mp0) REVERT: C 701 GLU cc_start: 0.8206 (mp0) cc_final: 0.7888 (mp0) REVERT: D 586 ARG cc_start: 0.8133 (mmm-85) cc_final: 0.7599 (mmm160) REVERT: I 207 PHE cc_start: 0.9022 (m-80) cc_final: 0.8799 (m-80) REVERT: J 145 VAL cc_start: 0.7466 (p) cc_final: 0.7232 (m) outliers start: 18 outliers final: 11 residues processed: 166 average time/residue: 0.2785 time to fit residues: 66.5408 Evaluate side-chains 162 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 150 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain I residue 183 ASN Chi-restraints excluded: chain J residue 183 ASN Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 789 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 chunk 168 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 152 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 178 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 710 GLN D 508 GLN ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13928 Z= 0.176 Angle : 0.488 11.860 19030 Z= 0.243 Chirality : 0.038 0.136 2270 Planarity : 0.003 0.067 2320 Dihedral : 6.006 88.204 2138 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.46 % Allowed : 20.45 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 1.23 (0.21), residues: 1880 helix: 2.31 (0.17), residues: 1070 sheet: -2.16 (0.47), residues: 134 loop : -1.04 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 767 HIS 0.003 0.001 HIS J 105 PHE 0.011 0.001 PHE I 207 TYR 0.016 0.001 TYR A 669 ARG 0.015 0.001 ARG I 97 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 152 time to evaluate : 1.603 Fit side-chains REVERT: A 395 THR cc_start: 0.9175 (OUTLIER) cc_final: 0.8933 (m) REVERT: A 701 GLU cc_start: 0.8279 (mp0) cc_final: 0.7986 (mp0) REVERT: C 701 GLU cc_start: 0.8203 (mp0) cc_final: 0.7892 (mp0) REVERT: D 586 ARG cc_start: 0.8129 (mmm-85) cc_final: 0.7529 (mmm160) REVERT: I 207 PHE cc_start: 0.9004 (m-80) cc_final: 0.8793 (m-80) REVERT: J 145 VAL cc_start: 0.7451 (p) cc_final: 0.7241 (m) outliers start: 17 outliers final: 13 residues processed: 161 average time/residue: 0.2725 time to fit residues: 63.1498 Evaluate side-chains 164 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 150 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain I residue 183 ASN Chi-restraints excluded: chain J residue 183 ASN Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 789 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 187 optimal weight: 0.5980 chunk 172 optimal weight: 4.9990 chunk 149 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 158 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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 D 508 GLN ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 13928 Z= 0.429 Angle : 0.608 13.023 19030 Z= 0.307 Chirality : 0.041 0.141 2270 Planarity : 0.004 0.064 2320 Dihedral : 6.530 84.152 2138 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.80 % Allowed : 20.10 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 0.89 (0.20), residues: 1880 helix: 2.07 (0.17), residues: 1046 sheet: -2.34 (0.45), residues: 142 loop : -1.08 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 578 HIS 0.002 0.001 HIS I 83 PHE 0.028 0.002 PHE I 165 TYR 0.017 0.002 TYR A 417 ARG 0.016 0.001 ARG I 97 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 145 time to evaluate : 1.467 Fit side-chains REVERT: A 395 THR cc_start: 0.9278 (OUTLIER) cc_final: 0.9058 (m) REVERT: A 701 GLU cc_start: 0.8249 (mp0) cc_final: 0.7939 (mp0) REVERT: C 701 GLU cc_start: 0.8218 (mp0) cc_final: 0.7895 (mp0) REVERT: D 586 ARG cc_start: 0.8143 (mmm-85) cc_final: 0.7520 (mmm160) REVERT: I 207 PHE cc_start: 0.9040 (m-80) cc_final: 0.8809 (m-80) REVERT: J 145 VAL cc_start: 0.7477 (p) cc_final: 0.7231 (m) REVERT: B 400 ILE cc_start: 0.7036 (mp) cc_final: 0.6748 (tt) outliers start: 21 outliers final: 18 residues processed: 157 average time/residue: 0.2884 time to fit residues: 64.4371 Evaluate side-chains 160 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 141 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain I residue 183 ASN Chi-restraints excluded: chain J residue 183 ASN Chi-restraints excluded: chain J residue 218 ILE Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 789 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 153 optimal weight: 0.0060 chunk 18 optimal weight: 0.5980 chunk 27 optimal weight: 7.9990 chunk 131 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 overall best weight: 1.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 710 GLN D 508 GLN ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.098875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.074891 restraints weight = 30830.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.076819 restraints weight = 19497.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.078152 restraints weight = 15112.903| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13928 Z= 0.270 Angle : 0.538 13.225 19030 Z= 0.269 Chirality : 0.039 0.137 2270 Planarity : 0.004 0.068 2320 Dihedral : 6.265 79.422 2138 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.98 % Allowed : 20.36 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.21), residues: 1880 helix: 2.12 (0.17), residues: 1060 sheet: -2.27 (0.47), residues: 134 loop : -1.01 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 574 HIS 0.002 0.001 HIS I 83 PHE 0.027 0.001 PHE I 165 TYR 0.016 0.001 TYR C 417 ARG 0.016 0.001 ARG I 97 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2463.76 seconds wall clock time: 45 minutes 17.79 seconds (2717.79 seconds total)