Starting phenix.real_space_refine on Sat Mar 16 04:14:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qhh_13972/03_2024/7qhh_13972_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qhh_13972/03_2024/7qhh_13972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qhh_13972/03_2024/7qhh_13972.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qhh_13972/03_2024/7qhh_13972.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qhh_13972/03_2024/7qhh_13972_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qhh_13972/03_2024/7qhh_13972_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 8884 2.51 5 N 2202 2.21 5 O 2478 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 541": "NH1" <-> "NH2" Residue "A PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 623": "OE1" <-> "OE2" Residue "A ASP 634": "OD1" <-> "OD2" Residue "A TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 684": "OE1" <-> "OE2" Residue "A TYR 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 431": "OE1" <-> "OE2" Residue "B PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 586": "NH1" <-> "NH2" Residue "B PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 719": "OD1" <-> "OD2" Residue "B PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 541": "NH1" <-> "NH2" Residue "C PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 623": "OE1" <-> "OE2" Residue "C ASP 634": "OD1" <-> "OD2" Residue "C TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 684": "OE1" <-> "OE2" Residue "C TYR 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 431": "OE1" <-> "OE2" Residue "D PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 586": "NH1" <-> "NH2" Residue "D PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 719": "OD1" <-> "OD2" Residue "D PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 231": "NH1" <-> "NH2" Residue "I TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 231": "NH1" <-> "NH2" Residue "A GLU 901": "OE1" <-> "OE2" Residue "C GLU 901": "OE1" <-> "OE2" 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: 13626 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 2682 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 130} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 385} Chain breaks: 2 Unresolved non-hydrogen bonds: 471 Unresolved non-hydrogen angles: 571 Unresolved non-hydrogen dihedrals: 393 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 10, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 17, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 223 Chain: "B" Number of atoms: 2691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 2691 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 133} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 Unresolved non-hydrogen bonds: 480 Unresolved non-hydrogen angles: 581 Unresolved non-hydrogen dihedrals: 404 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 2, 'GLU:plan': 18, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 222 Chain: "C" Number of atoms: 2682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 2682 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 130} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 385} Chain breaks: 2 Unresolved non-hydrogen bonds: 471 Unresolved non-hydrogen angles: 571 Unresolved non-hydrogen dihedrals: 393 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 10, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 17, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 223 Chain: "D" Number of atoms: 2691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 2691 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 133} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 Unresolved non-hydrogen bonds: 480 Unresolved non-hydrogen angles: 581 Unresolved non-hydrogen dihedrals: 404 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 2, 'GLU:plan': 18, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 222 Chain: "J" Number of atoms: 1282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1282 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 2, 'TRANS': 182} Chain breaks: 2 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 4, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 90 Chain: "I" Number of atoms: 1282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1282 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 2, 'TRANS': 182} Chain breaks: 2 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 4, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 90 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 71 Unusual residues: {'OLC': 1, 'PAM': 2} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {'79N': 1, 'PAM': 1} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain: "C" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 71 Unusual residues: {'OLC': 1, 'PAM': 2} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Chain: "D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {'79N': 1, 'PAM': 1} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain: "J" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'PAM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'PAM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.06, per 1000 atoms: 0.59 Number of scatterers: 13626 At special positions: 0 Unit cell: (124.02, 109.18, 133.56, 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 62 16.00 O 2478 8.00 N 2202 7.00 C 8884 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=2.04 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 714 " - pdb=" SG CYS C 769 " distance=2.04 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS J 52 " - pdb=" SG CYS J 91 " distance=2.04 Simple disulfide: pdb=" SG CYS J 90 " - pdb=" SG CYS J 100 " distance=2.06 Simple disulfide: pdb=" SG CYS I 52 " - pdb=" SG CYS I 91 " distance=2.04 Simple disulfide: pdb=" SG CYS I 90 " - pdb=" SG CYS I 100 " distance=2.06 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: 5.67 Conformation dependent library (CDL) restraints added in 2.5 seconds 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3612 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 70 helices and 18 sheets defined 51.5% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.62 Creating SS restraints... Processing helix chain 'A' and resid 420 through 432 Processing helix chain 'A' and resid 458 through 465 Processing helix chain 'A' and resid 479 through 484 removed outlier: 3.715A pdb=" N VAL A 484 " --> pdb=" O VAL A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 540 Processing helix chain 'A' and resid 569 through 581 Processing helix chain 'A' and resid 592 through 625 removed outlier: 3.512A pdb=" N VAL A 597 " --> pdb=" O SER A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 637 Processing helix chain 'A' and resid 650 through 657 Processing helix chain 'A' and resid 661 through 671 removed outlier: 3.562A pdb=" N LYS A 671 " --> pdb=" O TRP A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 Processing helix chain 'A' and resid 702 through 710 Processing helix chain 'A' and resid 737 through 752 Proline residue: A 741 - end of helix removed outlier: 3.659A pdb=" N LEU A 747 " --> pdb=" O ASN A 743 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER A 750 " --> pdb=" O VAL A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 766 Processing helix chain 'A' and resid 789 through 814 Processing helix chain 'B' and resid 417 through 420 removed outlier: 3.980A pdb=" N ARG B 420 " --> pdb=" O GLY B 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 417 through 420' Processing helix chain 'B' and resid 424 through 436 Processing helix chain 'B' and resid 463 through 469 Processing helix chain 'B' and resid 483 through 488 removed outlier: 3.704A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) 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 removed outlier: 3.545A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 642 Processing helix chain 'B' and resid 654 through 661 Processing helix chain 'B' and resid 665 through 675 Processing helix chain 'B' and resid 686 through 696 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 741 through 756 Proline residue: B 745 - end of helix Processing helix chain 'B' and resid 758 through 767 Processing helix chain 'B' and resid 793 through 818 Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 458 through 465 Processing helix chain 'C' and resid 479 through 484 removed outlier: 3.715A pdb=" N VAL C 484 " --> pdb=" O VAL C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 540 Processing helix chain 'C' and resid 569 through 581 Processing helix chain 'C' and resid 592 through 625 removed outlier: 3.512A pdb=" N VAL C 597 " --> pdb=" O SER C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 637 Processing helix chain 'C' and resid 650 through 657 Processing helix chain 'C' and resid 661 through 671 removed outlier: 3.561A pdb=" N LYS C 671 " --> pdb=" O TRP C 667 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 692 Processing helix chain 'C' and resid 702 through 710 Processing helix chain 'C' and resid 737 through 752 Proline residue: C 741 - end of helix removed outlier: 3.659A pdb=" N LEU C 747 " --> pdb=" O ASN C 743 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER C 750 " --> pdb=" O VAL C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 766 Processing helix chain 'C' and resid 789 through 814 Processing helix chain 'D' and resid 417 through 420 removed outlier: 3.980A pdb=" N ARG D 420 " --> pdb=" O GLY D 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 417 through 420' Processing helix chain 'D' and resid 424 through 436 Processing helix chain 'D' and resid 463 through 469 Processing helix chain 'D' and resid 483 through 488 removed outlier: 3.703A pdb=" N VAL D 488 " --> pdb=" O VAL D 484 " (cutoff:3.500A) 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 removed outlier: 3.544A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 642 Processing helix chain 'D' and resid 654 through 661 Processing helix chain 'D' and resid 665 through 675 Processing helix chain 'D' and resid 686 through 696 Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 741 through 756 Proline residue: D 745 - end of helix Processing helix chain 'D' and resid 758 through 767 Processing helix chain 'D' and resid 793 through 818 Processing helix chain 'J' and resid 17 through 40 removed outlier: 3.554A pdb=" N VAL J 21 " --> pdb=" O LYS J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 117 through 127 Processing helix chain 'J' and resid 129 through 150 removed outlier: 3.652A pdb=" N ALA J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG J 149 " --> pdb=" O VAL J 145 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL J 150 " --> pdb=" O ALA J 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 156 through 184 Processing helix chain 'J' and resid 203 through 233 Processing helix chain 'I' and resid 17 through 40 removed outlier: 3.555A pdb=" N VAL I 21 " --> pdb=" O LYS I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 127 Processing helix chain 'I' and resid 129 through 150 removed outlier: 3.652A pdb=" N ALA I 146 " --> pdb=" O GLY I 142 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG I 149 " --> pdb=" O VAL I 145 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL I 150 " --> pdb=" O ALA I 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 156 through 184 Processing helix chain 'I' and resid 203 through 233 Processing sheet with id= A, first strand: chain 'A' and resid 391 through 394 Processing sheet with id= B, first strand: chain 'A' and resid 485 through 487 Processing sheet with id= C, first strand: chain 'A' and resid 492 through 495 removed outlier: 4.050A pdb=" N MET A 492 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 717 through 719 removed outlier: 4.471A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ALA A 642 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU A 699 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLY A 644 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N GLU A 701 " --> pdb=" O GLY A 644 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 395 through 398 Processing sheet with id= F, first strand: chain 'B' and resid 489 through 491 Processing sheet with id= G, first strand: chain 'B' and resid 496 through 499 removed outlier: 3.738A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 720 through 723 removed outlier: 3.977A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 9.448A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 391 through 394 Processing sheet with id= J, first strand: chain 'C' and resid 485 through 487 Processing sheet with id= K, first strand: chain 'C' and resid 492 through 495 removed outlier: 4.050A pdb=" N MET C 492 " --> pdb=" O TYR C 728 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 717 through 719 removed outlier: 4.470A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 395 through 398 Processing sheet with id= N, first strand: chain 'D' and resid 489 through 491 Processing sheet with id= O, first strand: chain 'D' and resid 496 through 499 removed outlier: 3.738A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 720 through 723 removed outlier: 3.978A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 9.450A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'J' and resid 199 through 201 Processing sheet with id= R, first strand: chain 'I' and resid 199 through 201 792 hydrogen bonds defined for protein. 2358 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: 3.72 Time building geometry restraints manager: 6.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2224 1.32 - 1.45: 3822 1.45 - 1.57: 7764 1.57 - 1.70: 0 1.70 - 1.83: 90 Bond restraints: 13900 Sorted by residual: bond pdb=" C LYS A 726 " pdb=" O LYS A 726 " ideal model delta sigma weight residual 1.234 1.282 -0.048 1.26e-02 6.30e+03 1.45e+01 bond pdb=" C LYS C 726 " pdb=" O LYS C 726 " ideal model delta sigma weight residual 1.234 1.282 -0.048 1.26e-02 6.30e+03 1.44e+01 bond pdb=" CA SER C 512 " pdb=" CB SER C 512 " ideal model delta sigma weight residual 1.532 1.472 0.060 1.65e-02 3.67e+03 1.33e+01 bond pdb=" N ILE A 485 " pdb=" CA ILE A 485 " ideal model delta sigma weight residual 1.458 1.501 -0.043 1.19e-02 7.06e+03 1.31e+01 bond pdb=" CA SER A 512 " pdb=" CB SER A 512 " ideal model delta sigma weight residual 1.532 1.472 0.060 1.65e-02 3.67e+03 1.31e+01 ... (remaining 13895 not shown) Histogram of bond angle deviations from ideal: 98.44 - 105.72: 248 105.72 - 113.00: 7104 113.00 - 120.28: 6306 120.28 - 127.56: 5220 127.56 - 134.84: 94 Bond angle restraints: 18972 Sorted by residual: angle pdb=" CA GLY B 465 " pdb=" C GLY B 465 " pdb=" O GLY B 465 " ideal model delta sigma weight residual 120.75 114.86 5.89 1.03e+00 9.43e-01 3.27e+01 angle pdb=" CA GLY D 465 " pdb=" C GLY D 465 " pdb=" O GLY D 465 " ideal model delta sigma weight residual 120.75 114.88 5.87 1.03e+00 9.43e-01 3.24e+01 angle pdb=" C VAL B 464 " pdb=" N GLY B 465 " pdb=" CA GLY B 465 " ideal model delta sigma weight residual 119.98 125.83 -5.85 1.11e+00 8.12e-01 2.78e+01 angle pdb=" C VAL D 464 " pdb=" N GLY D 465 " pdb=" CA GLY D 465 " ideal model delta sigma weight residual 119.98 125.82 -5.84 1.11e+00 8.12e-01 2.76e+01 angle pdb=" CA GLY C 495 " pdb=" C GLY C 495 " pdb=" O GLY C 495 " ideal model delta sigma weight residual 121.19 116.63 4.56 9.10e-01 1.21e+00 2.52e+01 ... (remaining 18967 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.86: 7674 25.86 - 51.72: 228 51.72 - 77.58: 26 77.58 - 103.45: 4 103.45 - 129.31: 4 Dihedral angle restraints: 7936 sinusoidal: 2280 harmonic: 5656 Sorted by residual: dihedral pdb=" CB CYS D 718 " pdb=" SG CYS D 718 " pdb=" SG CYS D 773 " pdb=" CB CYS D 773 " ideal model delta sinusoidal sigma weight residual 93.00 156.95 -63.95 1 1.00e+01 1.00e-02 5.38e+01 dihedral pdb=" CB CYS B 718 " pdb=" SG CYS B 718 " pdb=" SG CYS B 773 " pdb=" CB CYS B 773 " ideal model delta sinusoidal sigma weight residual 93.00 156.94 -63.94 1 1.00e+01 1.00e-02 5.38e+01 dihedral pdb=" C24 OLC A 903 " pdb=" C21 OLC A 903 " pdb=" C22 OLC A 903 " pdb=" O20 OLC A 903 " ideal model delta sinusoidal sigma weight residual 182.78 53.47 129.31 1 3.00e+01 1.11e-03 1.74e+01 ... (remaining 7933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 966 0.060 - 0.119: 858 0.119 - 0.178: 362 0.178 - 0.238: 50 0.238 - 0.297: 10 Chirality restraints: 2246 Sorted by residual: chirality pdb=" CA VAL D 626 " pdb=" N VAL D 626 " pdb=" C VAL D 626 " pdb=" CB VAL D 626 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA VAL B 626 " pdb=" N VAL B 626 " pdb=" C VAL B 626 " pdb=" CB VAL B 626 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CA ILE C 587 " pdb=" N ILE C 587 " pdb=" C ILE C 587 " pdb=" CB ILE C 587 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 2243 not shown) Planarity restraints: 2414 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 79N D 902 " 0.138 2.00e-02 2.50e+03 1.40e-01 1.95e+02 pdb=" C7 79N D 902 " 0.141 2.00e-02 2.50e+03 pdb=" C8 79N D 902 " -0.148 2.00e-02 2.50e+03 pdb=" C9 79N D 902 " -0.131 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 79N B 902 " -0.137 2.00e-02 2.50e+03 1.39e-01 1.94e+02 pdb=" C7 79N B 902 " -0.141 2.00e-02 2.50e+03 pdb=" C8 79N B 902 " 0.148 2.00e-02 2.50e+03 pdb=" C9 79N B 902 " 0.131 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PAM I1502 " 0.143 2.00e-02 2.50e+03 1.09e-01 1.18e+02 pdb=" C11 PAM I1502 " -0.057 2.00e-02 2.50e+03 pdb=" C8 PAM I1502 " 0.057 2.00e-02 2.50e+03 pdb=" C9 PAM I1502 " -0.143 2.00e-02 2.50e+03 ... (remaining 2411 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 7335 3.02 - 3.49: 15222 3.49 - 3.96: 21774 3.96 - 4.43: 24670 4.43 - 4.90: 39222 Nonbonded interactions: 108223 Sorted by model distance: nonbonded pdb=" O TRP D 606 " pdb=" OG1 THR D 609 " model vdw 2.546 2.440 nonbonded pdb=" O TRP B 606 " pdb=" OG1 THR B 609 " model vdw 2.546 2.440 nonbonded pdb=" O GLN J 20 " pdb=" OG1 THR J 24 " model vdw 2.569 2.440 nonbonded pdb=" O GLN I 20 " pdb=" OG1 THR I 24 " model vdw 2.569 2.440 nonbonded pdb=" N ILE A 587 " pdb=" O ILE A 587 " model vdw 2.569 2.496 ... (remaining 108218 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 390 or resid 393 through 394 or (resid 395 through 398 and \ (name N or name CA or name C or name O or name CB )) or resid 400 or (resid 401 \ and (name N or name CA or name C or name O or name CB )) or resid 402 through 4 \ 03 or resid 405 through 407 or resid 412 through 414 or (resid 416 and (name N o \ r name CA or name C or name O or name CB )) or resid 417 through 422 or (resid 4 \ 24 through 426 and (name N or name CA or name C or name O or name CB )) or resid \ 427 through 431 or resid 433 or resid 436 or resid 438 or resid 440 or (resid 4 \ 41 and (name N or name CA or name C or name O or name CB )) or (resid 443 and (n \ ame N or name CA or name C or name O or name CB )) or (resid 444 through 446 and \ (name N or name CA or name C or name O or name CB )) or (resid 447 through 450 \ and (name N or name CA or name C or name O or name CB )) or (resid 452 through 4 \ 54 and (name N or name CA or name C or name O or name CB )) or (resid 456 throug \ h 460 and (name N or name CA or name C or name O or name CB )) or (resid 461 thr \ ough 465 and (name N or name CA or name C or name O or name CB )) or resid 466 o \ r resid 468 through 469 or resid 471 or resid 473 through 478 or (resid 479 thro \ ugh 486 and (name N or name CA or name C or name O or name CB )) or resid 487 th \ rough 540 or (resid 541 through 543 and (name N or name CA or name C or name O o \ r name CB )) or resid 544 through 545 or (resid 566 and (name N or name CA or na \ me C or name O or name CB )) or resid 567 through 568 or (resid 569 and (name N \ or name CA or name C or name O or name CB )) or resid 570 through 581 or resid 5 \ 83 through 625 or (resid 626 and (name N or name CA or name C or name O or name \ CB )) or resid 627 through 633 or (resid 634 through 635 and (name N or name CA \ or name C or name O or name CB )) or resid 637 through 644 or (resid 645 and (na \ me N or name CA or name C or name O or name CB )) or resid 646 or resid 649 thro \ ugh 652 or (resid 653 and (name N or name CA or name C or name O or name CB )) o \ r resid 654 or (resid 655 through 659 and (name N or name CA or name C or name O \ or name CB )) or resid 660 through 661 or (resid 662 and (name N or name CA or \ name C or name O or name CB )) or resid 663 or (resid 665 through 668 and (name \ N or name CA or name C or name O or name CB )) or resid 669 through 670 or (resi \ d 672 through 674 and (name N or name CA or name C or name O or name CB )) or re \ sid 675 through 678 or (resid 679 through 680 and (name N or name CA or name C o \ r name O or name CB )) or resid 681 through 682 or (resid 684 and (name N or nam \ e CA or name C or name O or name CB )) or resid 685 or resid 688 through 698 or \ (resid 699 and (name N or name CA or name C or name O or name CB )) or resid 700 \ through 701 or (resid 702 and (name N or name CA or name C or name O or name CB \ )) or resid 703 through 707 or (resid 708 through 712 and (name N or name CA or \ name C or name O or name CB )) or resid 713 through 717 or (resid 718 and (name \ N or name CA or name C or name O or name CB )) or resid 719 through 722 or (res \ id 723 and (name N or name CA or name C or name O or name CB )) or resid 724 thr \ ough 735 or (resid 736 and (name N or name CA or name C or name O or name CB )) \ or resid 738 or resid 741 or (resid 742 through 752 and (name N or name CA or na \ me C or name O or name CB )) or resid 753 through 759 or resid 761 through 795 o \ r resid 797 through 815 or resid 901)) selection = (chain 'B' and ((resid 394 and (name N or name CA or name C or name O or name CB \ )) or resid 397 through 399 or (resid 400 through 402 and (name N or name CA or \ name C or name O or name CB )) or resid 404 through 407 or resid 409 through 41 \ 1 or resid 416 through 418 or resid 420 through 421 or (resid 422 and (name N or \ name CA or name C or name O or name CB )) or resid 423 through 426 or resid 428 \ through 434 or (resid 435 and (name N or name CA or name C or name O or name CB \ )) or resid 437 or resid 440 or (resid 442 and (name N or name CA or name C or \ name O or name CB )) or resid 444 through 445 or resid 447 through 454 or resid \ 456 through 458 or (resid 460 through 461 and (name N or name CA or name C or na \ me O or name CB )) or (resid 462 through 469 and (name N or name CA or name C or \ name O or name CB )) or resid 470 or resid 472 through 473 or resid 475 or resi \ d 477 through 478 or (resid 479 and (name N or name CA or name C or name O or na \ me CB )) or resid 480 or (resid 481 and (name N or name CA or name C or name O o \ r name CB )) or resid 482 through 483 or (resid 484 through 490 and (name N or n \ ame CA or name C or name O or name CB )) or resid 491 through 492 or (resid 493 \ and (name N or name CA or name C or name O or name CB )) or resid 494 through 50 \ 0 or (resid 501 through 503 and (name N or name CA or name C or name O or name C \ B )) or resid 504 through 545 or (resid 546 through 547 and (name N or name CA o \ r name C or name O or name CB )) or resid 548 through 585 or resid 587 through 6 \ 33 or (resid 634 and (name N or name CA or name C or name O or name CB )) or res \ id 635 through 638 or (resid 639 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 641 through 642 and (name N or name CA or name C or name O o \ r name CB )) or resid 643 through 650 or resid 653 through 654 or (resid 655 thr \ ough 657 and (name N or name CA or name C or name O or name CB )) or resid 658 t \ hrough 660 or (resid 661 through 663 and (name N or name CA or name C or name O \ or name CB )) or resid 664 through 667 or resid 669 through 674 or resid 676 thr \ ough 679 or (resid 680 through 681 and (name N or name CA or name C or name O or \ name CB )) or resid 682 through 685 or (resid 686 and (name N or name CA or nam \ e C or name O or name CB )) or resid 688 through 689 or resid 692 through 718 or \ (resid 719 through 722 and (name N or name CA or name C or name O or name CB )) \ or resid 723 through 725 or (resid 726 through 727 and (name N or name CA or na \ me C or name O or name CB )) or resid 728 through 729 or (resid 730 and (name N \ or name CA or name C or name O or name CB )) or resid 731 through 733 or (resid \ 734 through 736 and (name N or name CA or name C or name O or name CB )) or resi \ d 737 through 740 or resid 742 or resid 745 through 746 or (resid 747 through 75 \ 6 and (name N or name CA or name C or name O or name CB )) or (resid 757 through \ 763 and (name N or name CA or name C or name O or name CB )) or resid 765 throu \ gh 767 or (resid 768 through 770 and (name N or name CA or name C or name O or n \ ame CB )) or resid 771 through 774 or resid 777 through 781 or resid 784 through \ 799 or resid 801 through 813 or (resid 814 and (name N or name CA or name C or \ name O or name CB )) or resid 815 through 817 or (resid 818 through 819 and (nam \ e N or name CA or name C or name O or name CB )) or resid 901)) selection = (chain 'C' and (resid 390 or resid 393 through 394 or (resid 395 through 398 and \ (name N or name CA or name C or name O or name CB )) or resid 400 or (resid 401 \ and (name N or name CA or name C or name O or name CB )) or resid 402 through 4 \ 03 or resid 405 through 407 or resid 412 through 414 or (resid 416 and (name N o \ r name CA or name C or name O or name CB )) or resid 417 through 422 or (resid 4 \ 24 through 426 and (name N or name CA or name C or name O or name CB )) or resid \ 427 through 431 or resid 433 or resid 436 or resid 438 or resid 440 or (resid 4 \ 41 and (name N or name CA or name C or name O or name CB )) or (resid 443 and (n \ ame N or name CA or name C or name O or name CB )) or (resid 444 through 446 and \ (name N or name CA or name C or name O or name CB )) or (resid 447 through 450 \ and (name N or name CA or name C or name O or name CB )) or (resid 452 through 4 \ 54 and (name N or name CA or name C or name O or name CB )) or (resid 456 throug \ h 460 and (name N or name CA or name C or name O or name CB )) or (resid 461 thr \ ough 465 and (name N or name CA or name C or name O or name CB )) or resid 466 o \ r resid 468 through 469 or resid 471 or resid 473 through 478 or (resid 479 thro \ ugh 486 and (name N or name CA or name C or name O or name CB )) or resid 487 th \ rough 540 or (resid 541 through 543 and (name N or name CA or name C or name O o \ r name CB )) or resid 544 through 545 or (resid 566 and (name N or name CA or na \ me C or name O or name CB )) or resid 567 through 568 or (resid 569 and (name N \ or name CA or name C or name O or name CB )) or resid 570 through 581 or resid 5 \ 83 through 625 or (resid 626 and (name N or name CA or name C or name O or name \ CB )) or resid 627 through 633 or (resid 634 through 635 and (name N or name CA \ or name C or name O or name CB )) or resid 637 through 644 or (resid 645 and (na \ me N or name CA or name C or name O or name CB )) or resid 646 or resid 649 thro \ ugh 652 or (resid 653 and (name N or name CA or name C or name O or name CB )) o \ r resid 654 or (resid 655 through 659 and (name N or name CA or name C or name O \ or name CB )) or resid 660 through 661 or (resid 662 and (name N or name CA or \ name C or name O or name CB )) or resid 663 or (resid 665 through 668 and (name \ N or name CA or name C or name O or name CB )) or resid 669 through 670 or (resi \ d 672 through 674 and (name N or name CA or name C or name O or name CB )) or re \ sid 675 through 678 or (resid 679 through 680 and (name N or name CA or name C o \ r name O or name CB )) or resid 681 through 682 or (resid 684 and (name N or nam \ e CA or name C or name O or name CB )) or resid 685 or resid 688 through 698 or \ (resid 699 and (name N or name CA or name C or name O or name CB )) or resid 700 \ through 701 or (resid 702 and (name N or name CA or name C or name O or name CB \ )) or resid 703 through 707 or (resid 708 through 712 and (name N or name CA or \ name C or name O or name CB )) or resid 713 through 717 or (resid 718 and (name \ N or name CA or name C or name O or name CB )) or resid 719 through 722 or (res \ id 723 and (name N or name CA or name C or name O or name CB )) or resid 724 thr \ ough 735 or (resid 736 and (name N or name CA or name C or name O or name CB )) \ or resid 738 or resid 741 or (resid 742 through 752 and (name N or name CA or na \ me C or name O or name CB )) or resid 753 through 759 or resid 761 through 795 o \ r resid 797 through 815 or resid 901)) selection = (chain 'D' and ((resid 394 and (name N or name CA or name C or name O or name CB \ )) or resid 397 through 399 or (resid 400 through 402 and (name N or name CA or \ name C or name O or name CB )) or resid 404 through 407 or resid 409 through 41 \ 1 or resid 416 through 418 or resid 420 through 421 or (resid 422 and (name N or \ name CA or name C or name O or name CB )) or resid 423 through 426 or resid 428 \ through 434 or (resid 435 and (name N or name CA or name C or name O or name CB \ )) or resid 437 or resid 440 or (resid 442 and (name N or name CA or name C or \ name O or name CB )) or resid 444 through 445 or resid 447 through 454 or resid \ 456 through 458 or (resid 460 through 461 and (name N or name CA or name C or na \ me O or name CB )) or (resid 462 through 469 and (name N or name CA or name C or \ name O or name CB )) or resid 470 or resid 472 through 473 or resid 475 or resi \ d 477 through 478 or (resid 479 and (name N or name CA or name C or name O or na \ me CB )) or resid 480 or (resid 481 and (name N or name CA or name C or name O o \ r name CB )) or resid 482 through 483 or (resid 484 through 490 and (name N or n \ ame CA or name C or name O or name CB )) or resid 491 through 492 or (resid 493 \ and (name N or name CA or name C or name O or name CB )) or resid 494 through 50 \ 0 or (resid 501 through 503 and (name N or name CA or name C or name O or name C \ B )) or resid 504 through 545 or (resid 546 through 547 and (name N or name CA o \ r name C or name O or name CB )) or resid 548 through 585 or resid 587 through 6 \ 33 or (resid 634 and (name N or name CA or name C or name O or name CB )) or res \ id 635 through 638 or (resid 639 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 641 through 642 and (name N or name CA or name C or name O o \ r name CB )) or resid 643 through 650 or resid 653 through 654 or (resid 655 thr \ ough 657 and (name N or name CA or name C or name O or name CB )) or resid 658 t \ hrough 660 or (resid 661 through 663 and (name N or name CA or name C or name O \ or name CB )) or resid 664 through 667 or resid 669 through 674 or resid 676 thr \ ough 679 or (resid 680 through 681 and (name N or name CA or name C or name O or \ name CB )) or resid 682 through 685 or (resid 686 and (name N or name CA or nam \ e C or name O or name CB )) or resid 688 through 689 or resid 692 through 718 or \ (resid 719 through 722 and (name N or name CA or name C or name O or name CB )) \ or resid 723 through 725 or (resid 726 through 727 and (name N or name CA or na \ me C or name O or name CB )) or resid 728 through 729 or (resid 730 and (name N \ or name CA or name C or name O or name CB )) or resid 731 through 733 or (resid \ 734 through 736 and (name N or name CA or name C or name O or name CB )) or resi \ d 737 through 740 or resid 742 or resid 745 through 746 or (resid 747 through 75 \ 6 and (name N or name CA or name C or name O or name CB )) or (resid 757 through \ 763 and (name N or name CA or name C or name O or name CB )) or resid 765 throu \ gh 767 or (resid 768 through 770 and (name N or name CA or name C or name O or n \ ame CB )) or resid 771 through 774 or resid 777 through 781 or resid 784 through \ 799 or resid 801 through 813 or (resid 814 and (name N or name CA or name C or \ name O or name CB )) or resid 815 through 817 or (resid 818 through 819 and (nam \ e 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: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.730 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 39.060 Find NCS groups from input model: 1.070 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 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 : 0.014 0.060 13900 Z= 0.946 Angle : 1.829 6.433 18972 Z= 1.429 Chirality : 0.090 0.297 2246 Planarity : 0.010 0.140 2414 Dihedral : 13.085 129.307 4300 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 0.31 % Favored : 99.59 % Rotamer: Outliers : 0.19 % Allowed : 2.64 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.17), residues: 1942 helix: -0.13 (0.14), residues: 1094 sheet: -0.52 (0.39), residues: 168 loop : -1.05 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.008 TRP B 766 HIS 0.004 0.002 HIS J 198 PHE 0.036 0.005 PHE A 537 TYR 0.046 0.006 TYR B 732 ARG 0.014 0.001 ARG D 694 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 374 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 478 THR cc_start: 0.6900 (p) cc_final: 0.6577 (t) REVERT: A 581 MET cc_start: 0.8199 (mmt) cc_final: 0.7845 (mmt) REVERT: A 646 LEU cc_start: 0.8022 (tp) cc_final: 0.7560 (mt) REVERT: A 663 PHE cc_start: 0.8822 (m-80) cc_final: 0.8581 (m-80) REVERT: A 678 PHE cc_start: 0.7432 (m-80) cc_final: 0.7151 (m-80) REVERT: A 705 ASN cc_start: 0.7677 (t0) cc_final: 0.6989 (t0) REVERT: B 661 ARG cc_start: 0.8634 (ptt180) cc_final: 0.8370 (ptt90) REVERT: B 704 LEU cc_start: 0.8572 (pt) cc_final: 0.8111 (tp) REVERT: B 764 ASN cc_start: 0.7113 (m-40) cc_final: 0.6598 (m-40) REVERT: B 769 ASP cc_start: 0.8477 (m-30) cc_final: 0.7694 (m-30) REVERT: C 416 ARG cc_start: 0.6802 (ttp-170) cc_final: 0.5770 (tpt90) REVERT: C 478 THR cc_start: 0.6917 (p) cc_final: 0.6598 (t) REVERT: C 581 MET cc_start: 0.8198 (mmt) cc_final: 0.7857 (mmt) REVERT: C 646 LEU cc_start: 0.8087 (tp) cc_final: 0.7656 (mt) REVERT: C 663 PHE cc_start: 0.8807 (m-80) cc_final: 0.8558 (m-80) REVERT: C 678 PHE cc_start: 0.7512 (m-80) cc_final: 0.7199 (m-80) REVERT: C 705 ASN cc_start: 0.7573 (t0) cc_final: 0.6767 (t0) REVERT: D 661 ARG cc_start: 0.8645 (ptt180) cc_final: 0.8440 (ptt90) REVERT: D 704 LEU cc_start: 0.8567 (pt) cc_final: 0.8080 (tp) REVERT: D 764 ASN cc_start: 0.7028 (m-40) cc_final: 0.6542 (m-40) REVERT: D 769 ASP cc_start: 0.8467 (m-30) cc_final: 0.7707 (m-30) outliers start: 2 outliers final: 0 residues processed: 374 average time/residue: 0.2600 time to fit residues: 137.4294 Evaluate side-chains 243 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 0.8980 chunk 148 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 100 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 chunk 153 optimal weight: 8.9990 chunk 59 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 chunk 114 optimal weight: 9.9990 chunk 177 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 GLN ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 587 GLN J 198 HIS I 198 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13900 Z= 0.193 Angle : 0.497 7.736 18972 Z= 0.264 Chirality : 0.039 0.153 2246 Planarity : 0.003 0.034 2414 Dihedral : 9.075 66.924 2300 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Rotamer: Outliers : 1.32 % Allowed : 13.40 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.19), residues: 1942 helix: 2.74 (0.15), residues: 1126 sheet: -0.53 (0.37), residues: 194 loop : -0.61 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 766 HIS 0.006 0.002 HIS J 198 PHE 0.013 0.001 PHE A 527 TYR 0.017 0.002 TYR B 816 ARG 0.002 0.000 ARG A 416 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 271 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 THR cc_start: 0.3623 (t) cc_final: 0.3379 (m) REVERT: A 415 ASP cc_start: 0.7277 (m-30) cc_final: 0.7064 (t0) REVERT: A 623 GLU cc_start: 0.6005 (mt-10) cc_final: 0.5791 (mt-10) REVERT: A 646 LEU cc_start: 0.7935 (tp) cc_final: 0.7584 (mt) REVERT: A 663 PHE cc_start: 0.8778 (m-80) cc_final: 0.8533 (m-80) REVERT: A 678 PHE cc_start: 0.7887 (m-80) cc_final: 0.7618 (m-80) REVERT: B 661 ARG cc_start: 0.8539 (ptt180) cc_final: 0.8149 (pmt170) REVERT: B 694 ARG cc_start: 0.8183 (mtt90) cc_final: 0.7915 (ttm110) REVERT: B 813 GLU cc_start: 0.7174 (mm-30) cc_final: 0.6878 (mm-30) REVERT: C 416 ARG cc_start: 0.6751 (ttp-170) cc_final: 0.5868 (tpt90) REVERT: C 646 LEU cc_start: 0.7964 (tp) cc_final: 0.7610 (mt) REVERT: C 663 PHE cc_start: 0.8762 (m-80) cc_final: 0.8066 (m-80) REVERT: C 678 PHE cc_start: 0.7858 (m-80) cc_final: 0.7582 (m-80) REVERT: C 723 LEU cc_start: 0.8704 (mp) cc_final: 0.7827 (tt) REVERT: D 460 TRP cc_start: 0.7445 (m-90) cc_final: 0.7168 (m-90) REVERT: D 661 ARG cc_start: 0.8558 (ptt180) cc_final: 0.8170 (pmt170) REVERT: D 694 ARG cc_start: 0.8197 (mtt90) cc_final: 0.7959 (ttm110) REVERT: D 813 GLU cc_start: 0.7130 (mm-30) cc_final: 0.6841 (mm-30) outliers start: 14 outliers final: 5 residues processed: 280 average time/residue: 0.2462 time to fit residues: 100.6874 Evaluate side-chains 251 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 246 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 144 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.7980 chunk 55 optimal weight: 9.9990 chunk 148 optimal weight: 8.9990 chunk 121 optimal weight: 20.0000 chunk 49 optimal weight: 0.6980 chunk 178 optimal weight: 8.9990 chunk 192 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 143 optimal weight: 20.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13900 Z= 0.232 Angle : 0.470 6.044 18972 Z= 0.246 Chirality : 0.039 0.145 2246 Planarity : 0.003 0.035 2414 Dihedral : 7.870 54.700 2300 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 2.08 % Allowed : 14.43 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.19), residues: 1942 helix: 3.05 (0.15), residues: 1114 sheet: -1.05 (0.36), residues: 196 loop : -0.33 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 766 HIS 0.002 0.001 HIS I 105 PHE 0.021 0.002 PHE I 165 TYR 0.025 0.001 TYR I 226 ARG 0.002 0.000 ARG A 416 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 268 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 MET cc_start: 0.7907 (mmt) cc_final: 0.7577 (mmt) REVERT: A 646 LEU cc_start: 0.7938 (tp) cc_final: 0.7602 (mt) REVERT: A 663 PHE cc_start: 0.8708 (m-80) cc_final: 0.8469 (m-80) REVERT: A 678 PHE cc_start: 0.7890 (m-80) cc_final: 0.7609 (m-80) REVERT: B 408 MET cc_start: 0.6107 (mmt) cc_final: 0.5791 (mmp) REVERT: B 661 ARG cc_start: 0.8360 (ptt180) cc_final: 0.8072 (pmt170) REVERT: B 694 ARG cc_start: 0.8191 (mtt90) cc_final: 0.7977 (ttm110) REVERT: B 726 ASN cc_start: 0.8719 (m-40) cc_final: 0.8352 (m-40) REVERT: B 767 TRP cc_start: 0.7447 (m-90) cc_final: 0.7147 (m-90) REVERT: B 813 GLU cc_start: 0.7230 (mm-30) cc_final: 0.6945 (mm-30) REVERT: C 416 ARG cc_start: 0.6605 (ttp-170) cc_final: 0.5750 (tpt90) REVERT: C 581 MET cc_start: 0.7902 (mmt) cc_final: 0.7573 (mmt) REVERT: C 646 LEU cc_start: 0.7971 (tp) cc_final: 0.7639 (mt) REVERT: C 663 PHE cc_start: 0.8746 (m-80) cc_final: 0.8481 (m-80) REVERT: C 678 PHE cc_start: 0.7882 (m-80) cc_final: 0.7575 (m-80) REVERT: D 408 MET cc_start: 0.6129 (mmt) cc_final: 0.5831 (mmp) REVERT: D 460 TRP cc_start: 0.7493 (m-90) cc_final: 0.7200 (m-90) REVERT: D 661 ARG cc_start: 0.8390 (ptt180) cc_final: 0.8090 (pmt170) REVERT: D 694 ARG cc_start: 0.8220 (mtt90) cc_final: 0.8009 (ttm110) REVERT: D 813 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6956 (mm-30) outliers start: 22 outliers final: 18 residues processed: 284 average time/residue: 0.2407 time to fit residues: 99.6907 Evaluate side-chains 260 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 242 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 143 VAL Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 143 VAL Chi-restraints excluded: chain I residue 144 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 85 optimal weight: 40.0000 chunk 119 optimal weight: 0.6980 chunk 178 optimal weight: 9.9990 chunk 189 optimal weight: 8.9990 chunk 93 optimal weight: 0.5980 chunk 169 optimal weight: 0.5980 chunk 51 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13900 Z= 0.166 Angle : 0.448 6.746 18972 Z= 0.233 Chirality : 0.038 0.141 2246 Planarity : 0.003 0.036 2414 Dihedral : 7.236 51.321 2300 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 1.60 % Allowed : 16.70 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.19), residues: 1942 helix: 3.00 (0.15), residues: 1112 sheet: -1.12 (0.36), residues: 196 loop : -0.25 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 766 HIS 0.002 0.001 HIS J 83 PHE 0.022 0.001 PHE I 165 TYR 0.027 0.001 TYR I 226 ARG 0.001 0.000 ARG A 416 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 259 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 646 LEU cc_start: 0.7905 (tp) cc_final: 0.7588 (mt) REVERT: A 678 PHE cc_start: 0.7880 (m-80) cc_final: 0.7599 (m-80) REVERT: A 762 TRP cc_start: 0.7819 (m100) cc_final: 0.7372 (m-10) REVERT: B 408 MET cc_start: 0.6048 (mmt) cc_final: 0.5746 (mmp) REVERT: B 661 ARG cc_start: 0.8355 (ptt180) cc_final: 0.8034 (pmt170) REVERT: B 813 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6917 (mm-30) REVERT: C 416 ARG cc_start: 0.6625 (ttp-170) cc_final: 0.5743 (tpt90) REVERT: C 646 LEU cc_start: 0.7944 (tp) cc_final: 0.7634 (mt) REVERT: C 663 PHE cc_start: 0.8729 (m-80) cc_final: 0.8422 (m-80) REVERT: C 678 PHE cc_start: 0.7867 (m-80) cc_final: 0.7584 (m-80) REVERT: C 762 TRP cc_start: 0.7525 (m100) cc_final: 0.6980 (m-10) REVERT: D 408 MET cc_start: 0.6103 (mmt) cc_final: 0.5836 (mmp) REVERT: D 460 TRP cc_start: 0.7544 (m-90) cc_final: 0.7276 (m-90) REVERT: D 661 ARG cc_start: 0.8368 (ptt180) cc_final: 0.8080 (pmt170) REVERT: D 813 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6937 (mm-30) outliers start: 17 outliers final: 12 residues processed: 268 average time/residue: 0.2357 time to fit residues: 92.9126 Evaluate side-chains 251 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 239 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 129 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 2 optimal weight: 30.0000 chunk 141 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 161 optimal weight: 6.9990 chunk 130 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 96 optimal weight: 2.9990 chunk 170 optimal weight: 0.1980 chunk 47 optimal weight: 30.0000 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 GLN ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13900 Z= 0.343 Angle : 0.513 9.886 18972 Z= 0.263 Chirality : 0.040 0.159 2246 Planarity : 0.003 0.036 2414 Dihedral : 7.894 56.836 2300 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 2.83 % Allowed : 16.98 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.19), residues: 1942 helix: 2.73 (0.15), residues: 1112 sheet: -1.24 (0.34), residues: 206 loop : -0.28 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 602 HIS 0.005 0.001 HIS I 83 PHE 0.035 0.002 PHE J 165 TYR 0.031 0.002 TYR I 226 ARG 0.003 0.000 ARG J 125 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 243 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 646 LEU cc_start: 0.8029 (tp) cc_final: 0.7679 (mt) REVERT: A 663 PHE cc_start: 0.8739 (m-80) cc_final: 0.8472 (m-80) REVERT: A 678 PHE cc_start: 0.7923 (m-80) cc_final: 0.7643 (m-80) REVERT: A 808 ILE cc_start: 0.8410 (mm) cc_final: 0.8116 (mt) REVERT: B 408 MET cc_start: 0.6031 (mmt) cc_final: 0.5740 (mmp) REVERT: B 813 GLU cc_start: 0.7300 (mm-30) cc_final: 0.7018 (mm-30) REVERT: C 416 ARG cc_start: 0.6722 (ttp-170) cc_final: 0.5797 (tpt90) REVERT: C 646 LEU cc_start: 0.8039 (tp) cc_final: 0.7705 (mt) REVERT: C 663 PHE cc_start: 0.8760 (m-80) cc_final: 0.8463 (m-80) REVERT: C 678 PHE cc_start: 0.7909 (m-80) cc_final: 0.7649 (m-80) REVERT: D 460 TRP cc_start: 0.7602 (m-90) cc_final: 0.7288 (m-90) REVERT: D 769 ASP cc_start: 0.8127 (m-30) cc_final: 0.7924 (m-30) REVERT: D 813 GLU cc_start: 0.7320 (mm-30) cc_final: 0.7046 (mm-30) outliers start: 30 outliers final: 20 residues processed: 266 average time/residue: 0.2223 time to fit residues: 88.6252 Evaluate side-chains 257 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 237 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 214 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 20.0000 chunk 170 optimal weight: 0.1980 chunk 37 optimal weight: 0.7980 chunk 111 optimal weight: 20.0000 chunk 46 optimal weight: 0.0050 chunk 189 optimal weight: 10.0000 chunk 157 optimal weight: 0.5980 chunk 87 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13900 Z= 0.140 Angle : 0.465 8.400 18972 Z= 0.232 Chirality : 0.038 0.154 2246 Planarity : 0.003 0.037 2414 Dihedral : 6.993 59.870 2300 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 2.36 % Allowed : 17.17 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.19), residues: 1942 helix: 2.91 (0.15), residues: 1114 sheet: -1.21 (0.35), residues: 202 loop : -0.29 (0.23), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 766 HIS 0.002 0.001 HIS J 105 PHE 0.038 0.001 PHE I 165 TYR 0.030 0.001 TYR I 226 ARG 0.001 0.000 ARG C 690 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 257 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 646 LEU cc_start: 0.7905 (tp) cc_final: 0.7641 (mt) REVERT: A 663 PHE cc_start: 0.8755 (m-80) cc_final: 0.8518 (m-80) REVERT: A 678 PHE cc_start: 0.7900 (m-80) cc_final: 0.7639 (m-80) REVERT: A 762 TRP cc_start: 0.7783 (m100) cc_final: 0.7351 (m-10) REVERT: A 808 ILE cc_start: 0.8328 (mm) cc_final: 0.8057 (mt) REVERT: B 408 MET cc_start: 0.5808 (mmt) cc_final: 0.5600 (mmp) REVERT: B 661 ARG cc_start: 0.8248 (ptt180) cc_final: 0.8006 (pmt170) REVERT: B 813 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6920 (mm-30) REVERT: C 416 ARG cc_start: 0.6820 (ttp-170) cc_final: 0.5954 (tpt90) REVERT: C 646 LEU cc_start: 0.7911 (tp) cc_final: 0.7664 (mt) REVERT: C 663 PHE cc_start: 0.8715 (m-80) cc_final: 0.8475 (m-80) REVERT: C 678 PHE cc_start: 0.7936 (m-80) cc_final: 0.7653 (m-80) REVERT: C 808 ILE cc_start: 0.8308 (mm) cc_final: 0.8065 (mt) REVERT: D 408 MET cc_start: 0.6198 (mmt) cc_final: 0.5902 (mmp) REVERT: D 661 ARG cc_start: 0.8274 (ptt180) cc_final: 0.8014 (pmt170) REVERT: D 769 ASP cc_start: 0.8067 (m-30) cc_final: 0.7834 (m-30) REVERT: D 813 GLU cc_start: 0.7234 (mm-30) cc_final: 0.6819 (mm-30) REVERT: J 231 ARG cc_start: 0.6676 (tpm170) cc_final: 0.6476 (tpm170) outliers start: 25 outliers final: 23 residues processed: 265 average time/residue: 0.2328 time to fit residues: 91.4827 Evaluate side-chains 270 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 247 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 655 PHE Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 214 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 105 optimal weight: 20.0000 chunk 188 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 115 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 587 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13900 Z= 0.364 Angle : 0.534 8.349 18972 Z= 0.269 Chirality : 0.041 0.180 2246 Planarity : 0.003 0.038 2414 Dihedral : 7.638 55.632 2300 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.49 % Allowed : 17.17 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.19), residues: 1942 helix: 2.50 (0.15), residues: 1130 sheet: -1.26 (0.34), residues: 206 loop : -0.29 (0.23), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 602 HIS 0.003 0.001 HIS I 83 PHE 0.035 0.002 PHE I 165 TYR 0.027 0.001 TYR I 226 ARG 0.003 0.000 ARG A 590 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 246 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 ASP cc_start: 0.7879 (m-30) cc_final: 0.7460 (p0) REVERT: A 646 LEU cc_start: 0.8037 (tp) cc_final: 0.7689 (mt) REVERT: A 663 PHE cc_start: 0.8750 (m-80) cc_final: 0.8523 (m-80) REVERT: A 678 PHE cc_start: 0.7941 (m-80) cc_final: 0.7725 (m-80) REVERT: A 762 TRP cc_start: 0.7719 (m100) cc_final: 0.7413 (m100) REVERT: B 460 TRP cc_start: 0.7657 (m-90) cc_final: 0.7210 (m-90) REVERT: B 767 TRP cc_start: 0.7360 (m-90) cc_final: 0.7082 (t-100) REVERT: B 813 GLU cc_start: 0.7295 (mm-30) cc_final: 0.7028 (mm-30) REVERT: C 415 ASP cc_start: 0.7943 (m-30) cc_final: 0.7538 (p0) REVERT: C 416 ARG cc_start: 0.6791 (ttp-170) cc_final: 0.5971 (tpt90) REVERT: C 646 LEU cc_start: 0.8045 (tp) cc_final: 0.7713 (mt) REVERT: C 663 PHE cc_start: 0.8749 (m-80) cc_final: 0.8511 (m-80) REVERT: C 678 PHE cc_start: 0.7951 (m-80) cc_final: 0.7673 (m-80) REVERT: C 808 ILE cc_start: 0.8442 (mm) cc_final: 0.8175 (mt) REVERT: D 460 TRP cc_start: 0.7728 (m-90) cc_final: 0.7366 (m-90) REVERT: D 767 TRP cc_start: 0.7396 (m-90) cc_final: 0.6936 (t-100) REVERT: D 769 ASP cc_start: 0.8122 (m-30) cc_final: 0.7908 (m-30) REVERT: D 813 GLU cc_start: 0.7297 (mm-30) cc_final: 0.7028 (mm-30) REVERT: J 231 ARG cc_start: 0.6714 (tpm170) cc_final: 0.6443 (tpm170) REVERT: D 901 GLU cc_start: 0.5815 (mm-30) cc_final: 0.5543 (mm-30) outliers start: 37 outliers final: 31 residues processed: 271 average time/residue: 0.2271 time to fit residues: 92.2939 Evaluate side-chains 272 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 241 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 655 PHE Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 214 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 0.5980 chunk 75 optimal weight: 6.9990 chunk 112 optimal weight: 50.0000 chunk 56 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 120 optimal weight: 20.0000 chunk 128 optimal weight: 6.9990 chunk 93 optimal weight: 0.5980 chunk 17 optimal weight: 0.2980 chunk 148 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7367 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13900 Z= 0.165 Angle : 0.475 7.876 18972 Z= 0.234 Chirality : 0.039 0.190 2246 Planarity : 0.003 0.038 2414 Dihedral : 6.822 55.564 2300 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 2.83 % Allowed : 18.40 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.19), residues: 1942 helix: 2.68 (0.15), residues: 1130 sheet: -1.19 (0.35), residues: 206 loop : -0.28 (0.23), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 766 HIS 0.001 0.001 HIS J 105 PHE 0.013 0.001 PHE J 165 TYR 0.023 0.001 TYR I 226 ARG 0.001 0.000 ARG A 541 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 255 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 646 LEU cc_start: 0.7970 (tp) cc_final: 0.7680 (mt) REVERT: A 678 PHE cc_start: 0.7981 (m-80) cc_final: 0.7749 (m-80) REVERT: A 762 TRP cc_start: 0.7759 (m100) cc_final: 0.7300 (m-10) REVERT: A 808 ILE cc_start: 0.8259 (mm) cc_final: 0.7932 (mt) REVERT: B 408 MET cc_start: 0.6066 (mmt) cc_final: 0.5782 (mmp) REVERT: B 813 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6983 (mm-30) REVERT: C 415 ASP cc_start: 0.7970 (m-30) cc_final: 0.7548 (p0) REVERT: C 416 ARG cc_start: 0.6867 (ttp-170) cc_final: 0.6074 (tpt90) REVERT: C 646 LEU cc_start: 0.7987 (tp) cc_final: 0.7700 (mt) REVERT: C 663 PHE cc_start: 0.8721 (m-80) cc_final: 0.8518 (m-80) REVERT: C 678 PHE cc_start: 0.7953 (m-80) cc_final: 0.7727 (m-80) REVERT: C 808 ILE cc_start: 0.8362 (mm) cc_final: 0.8107 (mt) REVERT: D 460 TRP cc_start: 0.7702 (m-90) cc_final: 0.7323 (m-90) REVERT: D 634 GLU cc_start: 0.5794 (pm20) cc_final: 0.5592 (pm20) REVERT: D 769 ASP cc_start: 0.7993 (m-30) cc_final: 0.7766 (m-30) REVERT: D 813 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6855 (mm-30) REVERT: D 901 GLU cc_start: 0.5788 (mm-30) cc_final: 0.5519 (mm-30) outliers start: 30 outliers final: 27 residues processed: 266 average time/residue: 0.2255 time to fit residues: 90.3501 Evaluate side-chains 270 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 243 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 655 PHE Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 214 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 0.6980 chunk 180 optimal weight: 4.9990 chunk 165 optimal weight: 9.9990 chunk 176 optimal weight: 3.9990 chunk 105 optimal weight: 20.0000 chunk 76 optimal weight: 20.0000 chunk 138 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 159 optimal weight: 0.8980 chunk 166 optimal weight: 6.9990 chunk 175 optimal weight: 0.9980 overall best weight: 1.4382 ------------------------------------------------------------------------------- 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: 0.7409 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13900 Z= 0.260 Angle : 0.512 7.769 18972 Z= 0.254 Chirality : 0.040 0.210 2246 Planarity : 0.003 0.038 2414 Dihedral : 6.924 55.460 2300 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.64 % Allowed : 19.25 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.19), residues: 1942 helix: 2.54 (0.15), residues: 1128 sheet: -1.25 (0.34), residues: 206 loop : -0.29 (0.23), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 766 HIS 0.002 0.001 HIS J 105 PHE 0.015 0.001 PHE I 165 TYR 0.047 0.001 TYR J 179 ARG 0.005 0.000 ARG B 661 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 252 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 646 LEU cc_start: 0.8012 (tp) cc_final: 0.7693 (mt) REVERT: A 678 PHE cc_start: 0.8004 (m-80) cc_final: 0.7704 (m-80) REVERT: A 723 LEU cc_start: 0.8591 (mt) cc_final: 0.7861 (tp) REVERT: A 762 TRP cc_start: 0.7718 (m100) cc_final: 0.7308 (m-10) REVERT: A 808 ILE cc_start: 0.8374 (mm) cc_final: 0.8058 (mt) REVERT: B 767 TRP cc_start: 0.7170 (m-90) cc_final: 0.6871 (t-100) REVERT: B 813 GLU cc_start: 0.7294 (mm-30) cc_final: 0.7038 (mm-30) REVERT: C 415 ASP cc_start: 0.7941 (m-30) cc_final: 0.7514 (p0) REVERT: C 416 ARG cc_start: 0.6817 (ttp-170) cc_final: 0.6006 (tpt90) REVERT: C 646 LEU cc_start: 0.8026 (tp) cc_final: 0.7717 (mt) REVERT: C 663 PHE cc_start: 0.8735 (m-80) cc_final: 0.8523 (m-80) REVERT: C 678 PHE cc_start: 0.7981 (m-80) cc_final: 0.7686 (m-80) REVERT: C 808 ILE cc_start: 0.8396 (mm) cc_final: 0.8145 (mt) REVERT: D 460 TRP cc_start: 0.7706 (m-90) cc_final: 0.7367 (m-90) REVERT: D 767 TRP cc_start: 0.7239 (m-90) cc_final: 0.6860 (t-100) REVERT: D 769 ASP cc_start: 0.7949 (m-30) cc_final: 0.7705 (m-30) REVERT: D 813 GLU cc_start: 0.7263 (mm-30) cc_final: 0.6869 (mm-30) REVERT: D 901 GLU cc_start: 0.5901 (mm-30) cc_final: 0.5645 (mm-30) outliers start: 28 outliers final: 27 residues processed: 266 average time/residue: 0.2209 time to fit residues: 88.4303 Evaluate side-chains 266 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 239 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 625 MET Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 655 PHE Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 214 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 4.9990 chunk 186 optimal weight: 5.9990 chunk 113 optimal weight: 20.0000 chunk 88 optimal weight: 20.0000 chunk 129 optimal weight: 9.9990 chunk 195 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 155 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 120 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 183 ASN I 183 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.070 13900 Z= 0.614 Angle : 0.690 8.404 18972 Z= 0.350 Chirality : 0.045 0.207 2246 Planarity : 0.004 0.039 2414 Dihedral : 8.344 58.720 2300 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.21 % Allowed : 18.68 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.19), residues: 1942 helix: 1.86 (0.15), residues: 1120 sheet: -1.08 (0.38), residues: 168 loop : -0.63 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP D 766 HIS 0.008 0.002 HIS I 83 PHE 0.022 0.003 PHE I 165 TYR 0.035 0.002 TYR J 179 ARG 0.004 0.001 ARG J 125 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 232 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 572 SER cc_start: 0.8553 (OUTLIER) cc_final: 0.8238 (t) REVERT: A 646 LEU cc_start: 0.8095 (tp) cc_final: 0.7756 (mt) REVERT: A 678 PHE cc_start: 0.7963 (m-80) cc_final: 0.7651 (m-80) REVERT: B 460 TRP cc_start: 0.7737 (m-90) cc_final: 0.7433 (m-90) REVERT: C 415 ASP cc_start: 0.7868 (m-30) cc_final: 0.7438 (p0) REVERT: C 416 ARG cc_start: 0.6903 (ttp-170) cc_final: 0.6054 (tpt90) REVERT: C 572 SER cc_start: 0.8555 (OUTLIER) cc_final: 0.8228 (t) REVERT: C 646 LEU cc_start: 0.8126 (tp) cc_final: 0.7798 (mt) REVERT: C 678 PHE cc_start: 0.7947 (m-80) cc_final: 0.7657 (m-80) REVERT: D 460 TRP cc_start: 0.7795 (m-90) cc_final: 0.7547 (m-90) REVERT: D 767 TRP cc_start: 0.7369 (m-90) cc_final: 0.7000 (t-100) REVERT: D 769 ASP cc_start: 0.7991 (m-30) cc_final: 0.7766 (m-30) outliers start: 34 outliers final: 27 residues processed: 251 average time/residue: 0.2212 time to fit residues: 83.5969 Evaluate side-chains 256 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 227 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 625 MET Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 214 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 6.9990 chunk 165 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 143 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 chunk 155 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 159 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 ASN ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.198003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.158006 restraints weight = 20344.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.150742 restraints weight = 28120.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.149344 restraints weight = 30638.779| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.086 13900 Z= 0.664 Angle : 0.710 8.747 18972 Z= 0.364 Chirality : 0.047 0.210 2246 Planarity : 0.004 0.039 2414 Dihedral : 8.699 59.098 2300 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.92 % Allowed : 18.77 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.19), residues: 1942 helix: 1.48 (0.15), residues: 1114 sheet: -1.41 (0.40), residues: 160 loop : -0.74 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP D 766 HIS 0.008 0.002 HIS I 83 PHE 0.023 0.003 PHE A 527 TYR 0.061 0.003 TYR I 179 ARG 0.007 0.001 ARG B 661 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2668.93 seconds wall clock time: 49 minutes 17.69 seconds (2957.69 seconds total)