Starting phenix.real_space_refine on Fri Feb 16 15:45:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ayn_15717/02_2024/8ayn_15717_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ayn_15717/02_2024/8ayn_15717.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ayn_15717/02_2024/8ayn_15717.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ayn_15717/02_2024/8ayn_15717.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ayn_15717/02_2024/8ayn_15717_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ayn_15717/02_2024/8ayn_15717_updated.pdb" } resolution = 2.8 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= 0.004 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 S 84 5.16 5 C 10336 2.51 5 N 2484 2.21 5 O 2824 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 427": "OD1" <-> "OD2" Residue "B TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 490": "OD1" <-> "OD2" Residue "B PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 586": "NH1" <-> "NH2" Residue "B PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 710": "OE1" <-> "OE2" Residue "B ASP 719": "OD1" <-> "OD2" Residue "B TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 427": "OD1" <-> "OD2" Residue "D TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 586": "NH1" <-> "NH2" Residue "D PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 651": "OD1" <-> "OD2" Residue "D ASP 668": "OD1" <-> "OD2" Residue "D TYR 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 710": "OE1" <-> "OE2" Residue "D TYR 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 728": "OD1" <-> "OD2" Residue "D TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 412": "OE1" <-> "OE2" Residue "C TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 418": "OE1" <-> "OE2" Residue "C TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 482": "OE1" <-> "OE2" Residue "C PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 515": "OD1" <-> "OD2" Residue "C TYR 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 640": "OE1" <-> "OE2" Residue "C TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 647": "OE1" <-> "OE2" Residue "C GLU 653": "OE1" <-> "OE2" Residue "C GLU 706": "OE1" <-> "OE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 709": "OE1" <-> "OE2" Residue "C ASP 724": "OD1" <-> "OD2" Residue "C GLU 751": "OE1" <-> "OE2" Residue "C GLU 768": "OE1" <-> "OE2" Residue "C GLU 809": "OE1" <-> "OE2" Residue "C PHE 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 399": "OD1" <-> "OD2" Residue "A TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 412": "OE1" <-> "OE2" Residue "A TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 418": "OE1" <-> "OE2" Residue "A TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 482": "OE1" <-> "OE2" Residue "A PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 515": "OD1" <-> "OD2" Residue "A TYR 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 640": "OE1" <-> "OE2" Residue "A TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 647": "OE1" <-> "OE2" Residue "A GLU 653": "OE1" <-> "OE2" Residue "A GLU 706": "OE1" <-> "OE2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 709": "OE1" <-> "OE2" Residue "A ASP 724": "OD1" <-> "OD2" Residue "A GLU 751": "OE1" <-> "OE2" Residue "A GLU 768": "OE1" <-> "OE2" Residue "A GLU 809": "OE1" <-> "OE2" Residue "A TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15748 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 3084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3084 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "I" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1358 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain breaks: 2 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 4, 'HIS:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 55 Chain: "J" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1358 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain breaks: 2 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 4, 'HIS:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 55 Chain: "D" Number of atoms: 3084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3084 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 3088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3088 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 392} Chain breaks: 2 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "A" Number of atoms: 3088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3088 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 392} Chain breaks: 2 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 122 Unusual residues: {'OLC': 1, 'PLM': 1, 'POV': 1, 'ZK1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'OLR': 1, 'PLM': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'OLR': 1, 'PLM': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 122 Unusual residues: {'OLC': 1, 'PLM': 1, 'POV': 1, 'ZK1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 159 Unusual residues: {'OLC': 1, 'PLM': 4, 'POV': 1, 'ZK1': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Chain: "A" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 159 Unusual residues: {'OLC': 1, 'PLM': 4, 'POV': 1, 'ZK1': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Time building chain proxies: 9.15, per 1000 atoms: 0.58 Number of scatterers: 15748 At special positions: 0 Unit cell: (133.75, 108.07, 133.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 84 16.00 P 8 15.00 F 12 9.00 O 2824 8.00 N 2484 7.00 C 10336 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS I 52 " - pdb=" SG CYS I 91 " distance=2.03 Simple disulfide: pdb=" SG CYS I 90 " - pdb=" SG CYS I 100 " distance=2.03 Simple disulfide: pdb=" SG CYS J 52 " - pdb=" SG CYS J 91 " distance=2.03 Simple disulfide: pdb=" SG CYS J 90 " - pdb=" SG CYS J 100 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 714 " - pdb=" SG CYS C 769 " distance=2.03 Simple disulfide: pdb=" SG CYS A 714 " - pdb=" SG CYS A 769 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.49 Conformation dependent library (CDL) restraints added in 2.9 seconds 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3640 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 75 helices and 18 sheets defined 49.9% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.13 Creating SS restraints... Processing helix chain 'B' and resid 424 through 436 Processing helix chain 'B' and resid 463 through 468 Processing helix chain 'B' and resid 483 through 486 No H-bonds generated for 'chain 'B' and resid 483 through 486' Processing helix chain 'B' and resid 516 through 518 No H-bonds generated for 'chain 'B' and resid 516 through 518' Processing helix chain 'B' and resid 523 through 546 Processing helix chain 'B' and resid 573 through 584 Processing helix chain 'B' and resid 596 through 625 Processing helix chain 'B' and resid 636 through 641 Processing helix chain 'B' and resid 654 through 660 Processing helix chain 'B' and resid 665 through 676 Processing helix chain 'B' and resid 686 through 695 Processing helix chain 'B' and resid 706 through 713 Processing helix chain 'B' and resid 742 through 756 removed outlier: 3.535A pdb=" N LEU B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 767 Processing helix chain 'B' and resid 789 through 817 removed outlier: 5.513A pdb=" N GLY B 794 " --> pdb=" O SER B 790 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL B 795 " --> pdb=" O ASN B 791 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 39 Processing helix chain 'I' and resid 117 through 127 Processing helix chain 'I' and resid 129 through 149 removed outlier: 3.731A pdb=" N ARG I 149 " --> pdb=" O VAL I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 156 through 183 Processing helix chain 'I' and resid 203 through 232 Processing helix chain 'J' and resid 17 through 39 Processing helix chain 'J' and resid 117 through 127 Processing helix chain 'J' and resid 129 through 149 removed outlier: 3.732A pdb=" N ARG J 149 " --> pdb=" O VAL J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 156 through 183 Processing helix chain 'J' and resid 203 through 232 Processing helix chain 'D' and resid 424 through 436 removed outlier: 3.539A pdb=" N HIS D 435 " --> pdb=" O GLU D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 468 Processing helix chain 'D' and resid 483 through 486 No H-bonds generated for 'chain 'D' and resid 483 through 486' Processing helix chain 'D' and resid 516 through 518 No H-bonds generated for 'chain 'D' and resid 516 through 518' Processing helix chain 'D' and resid 523 through 546 Processing helix chain 'D' and resid 573 through 584 Processing helix chain 'D' and resid 596 through 625 Processing helix chain 'D' and resid 637 through 641 Processing helix chain 'D' and resid 654 through 661 Processing helix chain 'D' and resid 665 through 676 Processing helix chain 'D' and resid 686 through 695 Processing helix chain 'D' and resid 706 through 714 removed outlier: 3.723A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 756 removed outlier: 3.591A pdb=" N LEU D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 767 Processing helix chain 'D' and resid 789 through 791 No H-bonds generated for 'chain 'D' and resid 789 through 791' Processing helix chain 'D' and resid 793 through 818 Processing helix chain 'C' and resid 413 through 416 Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 458 through 464 Processing helix chain 'C' and resid 479 through 484 removed outlier: 3.738A pdb=" N VAL C 484 " --> pdb=" O VAL C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 514 No H-bonds generated for 'chain 'C' and resid 512 through 514' Processing helix chain 'C' and resid 519 through 541 Processing helix chain 'C' and resid 544 through 546 No H-bonds generated for 'chain 'C' and resid 544 through 546' Processing helix chain 'C' and resid 569 through 580 Processing helix chain 'C' and resid 592 through 624 Processing helix chain 'C' and resid 632 through 637 Processing helix chain 'C' and resid 650 through 656 Processing helix chain 'C' and resid 661 through 671 Processing helix chain 'C' and resid 682 through 692 Processing helix chain 'C' and resid 702 through 710 Processing helix chain 'C' and resid 738 through 752 Processing helix chain 'C' and resid 754 through 763 Processing helix chain 'C' and resid 789 through 811 Processing helix chain 'A' and resid 413 through 416 removed outlier: 3.728A pdb=" N ARG A 416 " --> pdb=" O GLY A 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 413 through 416' Processing helix chain 'A' and resid 420 through 432 Processing helix chain 'A' and resid 458 through 464 Processing helix chain 'A' and resid 479 through 484 removed outlier: 3.750A pdb=" N VAL A 484 " --> pdb=" O VAL A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 514 No H-bonds generated for 'chain 'A' and resid 512 through 514' Processing helix chain 'A' and resid 519 through 541 Processing helix chain 'A' and resid 544 through 546 No H-bonds generated for 'chain 'A' and resid 544 through 546' Processing helix chain 'A' and resid 569 through 580 Processing helix chain 'A' and resid 592 through 624 Processing helix chain 'A' and resid 632 through 637 Processing helix chain 'A' and resid 650 through 656 Processing helix chain 'A' and resid 661 through 671 Processing helix chain 'A' and resid 682 through 692 Processing helix chain 'A' and resid 702 through 710 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 789 through 811 Processing sheet with id= A, first strand: chain 'B' and resid 396 through 399 removed outlier: 6.294A pdb=" N LYS B 441 " --> pdb=" O VAL B 397 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N THR B 399 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR B 443 " --> pdb=" O THR B 399 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.809A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 701 through 705 removed outlier: 3.993A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'I' and resid 81 through 84 removed outlier: 3.872A pdb=" N LEU I 45 " --> pdb=" O SER I 84 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'I' and resid 88 through 91 removed outlier: 3.617A pdb=" N CYS I 91 " --> pdb=" O VAL I 99 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL I 99 " --> pdb=" O CYS I 91 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'J' and resid 81 through 84 removed outlier: 3.872A pdb=" N LEU J 45 " --> pdb=" O SER J 84 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 88 through 91 removed outlier: 3.617A pdb=" N CYS J 91 " --> pdb=" O VAL J 99 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL J 99 " --> pdb=" O CYS J 91 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 396 through 399 removed outlier: 6.299A pdb=" N LYS D 441 " --> pdb=" O VAL D 397 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N THR D 399 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N THR D 443 " --> pdb=" O THR D 399 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.771A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 720 through 723 removed outlier: 4.263A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 391 through 393 Processing sheet with id= L, first strand: chain 'C' and resid 485 through 487 Processing sheet with id= M, first strand: chain 'C' and resid 492 through 494 removed outlier: 3.918A pdb=" N MET C 492 " --> pdb=" O TYR C 728 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C 494 " --> pdb=" O LYS C 726 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 717 through 719 removed outlier: 3.856A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 9.657A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 391 through 393 Processing sheet with id= P, first strand: chain 'A' and resid 485 through 487 Processing sheet with id= Q, first strand: chain 'A' and resid 492 through 494 removed outlier: 3.931A pdb=" N MET A 492 " --> pdb=" O TYR A 728 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 494 " --> pdb=" O LYS A 726 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 717 through 719 removed outlier: 4.036A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA A 642 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N LEU A 699 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLY A 644 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 9.682A pdb=" N GLU A 701 " --> pdb=" O GLY A 644 " (cutoff:3.500A) 754 hydrogen bonds defined for protein. 2241 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.53 Time building geometry restraints manager: 6.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.34: 4735 1.34 - 1.50: 5004 1.50 - 1.65: 6179 1.65 - 1.81: 142 1.81 - 1.97: 6 Bond restraints: 16066 Sorted by residual: bond pdb=" C1 OLR I 503 " pdb=" C7 OLR I 503 " ideal model delta sigma weight residual 1.382 1.662 -0.280 2.00e-02 2.50e+03 1.95e+02 bond pdb=" C1 OLR J 503 " pdb=" C7 OLR J 503 " ideal model delta sigma weight residual 1.382 1.661 -0.279 2.00e-02 2.50e+03 1.94e+02 bond pdb=" C1 OLR J 503 " pdb=" S1 OLR J 503 " ideal model delta sigma weight residual 1.746 1.971 -0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C1 OLR I 503 " pdb=" S1 OLR I 503 " ideal model delta sigma weight residual 1.746 1.970 -0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C2 OLR J 503 " pdb=" O1 OLR J 503 " ideal model delta sigma weight residual 1.205 1.397 -0.192 2.00e-02 2.50e+03 9.21e+01 ... (remaining 16061 not shown) Histogram of bond angle deviations from ideal: 88.37 - 99.56: 21 99.56 - 110.74: 5592 110.74 - 121.93: 13136 121.93 - 133.11: 2861 133.11 - 144.30: 52 Bond angle restraints: 21662 Sorted by residual: angle pdb=" C35 POV A 907 " pdb=" C36 POV A 907 " pdb=" C37 POV A 907 " ideal model delta sigma weight residual 113.93 140.63 -26.70 3.00e+00 1.11e-01 7.92e+01 angle pdb=" C35 POV C 907 " pdb=" C36 POV C 907 " pdb=" C37 POV C 907 " ideal model delta sigma weight residual 113.93 140.52 -26.59 3.00e+00 1.11e-01 7.85e+01 angle pdb=" CAR ZK1 D 901 " pdb=" CAS ZK1 D 901 " pdb=" CAZ ZK1 D 901 " ideal model delta sigma weight residual 119.91 144.30 -24.39 3.00e+00 1.11e-01 6.61e+01 angle pdb=" CAJ ZK1 D 901 " pdb=" CAS ZK1 D 901 " pdb=" CAZ ZK1 D 901 " ideal model delta sigma weight residual 120.43 96.40 24.03 3.00e+00 1.11e-01 6.42e+01 angle pdb=" CAI ZK1 D 901 " pdb=" CAR ZK1 D 901 " pdb=" NAX ZK1 D 901 " ideal model delta sigma weight residual 120.86 97.28 23.58 3.00e+00 1.11e-01 6.18e+01 ... (remaining 21657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.77: 9242 32.77 - 65.54: 265 65.54 - 98.31: 38 98.31 - 131.08: 4 131.08 - 163.85: 7 Dihedral angle restraints: 9556 sinusoidal: 3838 harmonic: 5718 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 93.00 135.84 -42.84 1 1.00e+01 1.00e-02 2.56e+01 dihedral pdb=" O20 OLC D 902 " pdb=" C21 OLC D 902 " pdb=" C22 OLC D 902 " pdb=" O23 OLC D 902 " ideal model delta sinusoidal sigma weight residual 302.77 138.92 163.85 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C29 POV B 904 " pdb="C210 POV B 904 " pdb="C211 POV B 904 " pdb="C212 POV B 904 " ideal model delta sinusoidal sigma weight residual 112.25 -84.78 -162.97 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 9553 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1926 0.059 - 0.119: 443 0.119 - 0.178: 22 0.178 - 0.238: 9 0.238 - 0.297: 4 Chirality restraints: 2404 Sorted by residual: chirality pdb=" C8 OLR J 503 " pdb=" C10 OLR J 503 " pdb=" C6 OLR J 503 " pdb=" C9 OLR J 503 " both_signs ideal model delta sigma weight residual False -2.44 -2.73 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C8 OLR I 503 " pdb=" C10 OLR I 503 " pdb=" C6 OLR I 503 " pdb=" C9 OLR I 503 " both_signs ideal model delta sigma weight residual False -2.44 -2.73 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CG LEU A 573 " pdb=" CB LEU A 573 " pdb=" CD1 LEU A 573 " pdb=" CD2 LEU A 573 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 2401 not shown) Planarity restraints: 2632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 736 " -0.071 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO D 737 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO D 737 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO D 737 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 399 " -0.034 5.00e-02 4.00e+02 5.06e-02 4.09e+00 pdb=" N PRO C 400 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 400 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 400 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 399 " -0.033 5.00e-02 4.00e+02 5.01e-02 4.01e+00 pdb=" N PRO A 400 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 400 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 400 " -0.024 5.00e-02 4.00e+02 ... (remaining 2629 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 126 2.58 - 3.16: 13627 3.16 - 3.74: 23364 3.74 - 4.32: 34147 4.32 - 4.90: 57374 Nonbonded interactions: 128638 Sorted by model distance: nonbonded pdb=" O PHE A 654 " pdb=" OG SER A 658 " model vdw 2.003 2.440 nonbonded pdb=" O PHE C 654 " pdb=" OG SER C 658 " model vdw 2.018 2.440 nonbonded pdb=" OG1 THR I 41 " pdb=" OG SER I 204 " model vdw 2.043 2.440 nonbonded pdb=" OG1 THR J 41 " pdb=" OG SER J 204 " model vdw 2.044 2.440 nonbonded pdb=" NH2 ARG B 715 " pdb=" O LYS B 770 " model vdw 2.064 2.520 ... (remaining 128633 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 398 or resid 400 through 403 or resid 405 thro \ ugh 406 or (resid 407 and (name N or name CA or name C or name O or name CB )) o \ r resid 412 through 414 or resid 416 through 422 or resid 424 through 431 or res \ id 433 or resid 436 or resid 438 or resid 440 through 441 or resid 443 through 4 \ 49 or (resid 450 and (name N or name CA or name C or name O or name CB )) or res \ id 452 through 453 or (resid 454 and (name N or name CA or name C or name O or n \ ame CB )) or resid 456 through 466 or resid 468 through 469 or resid 471 or resi \ d 473 through 546 or resid 567 through 581 or resid 583 through 635 or resid 637 \ through 646 or resid 649 through 663 or resid 665 through 670 or resid 672 thro \ ugh 682 or resid 684 through 685 or resid 688 through 692 or (resid 693 and (nam \ e N or name CA or name C or name O or name CB )) or resid 694 through 736 or res \ id 738 or resid 741 through 756 or (resid 757 and (name N or name CA or name C o \ r name O or name CB )) or resid 758 through 759 or resid 761 through 770 or (res \ id 772 through 773 and (name N or name CA or name C or name O or name CB )) or r \ esid 779 through 795 or resid 797 through 815 or resid 901 through 903)) selection = (chain 'B' and (resid 397 through 402 or resid 404 through 407 or resid 409 thro \ ugh 411 or resid 416 through 418 or resid 420 through 426 or resid 428 through 4 \ 35 or resid 437 or resid 440 or resid 442 or resid 444 through 445 or (resid 447 \ and (name N or name CA or name C or name O or name CB )) or resid 448 through 4 \ 54 or resid 456 through 458 or resid 460 through 470 or resid 472 through 473 or \ resid 475 or resid 477 through 508 or (resid 509 and (name N or name CA or name \ C or name O or name CB )) or resid 510 or (resid 511 and (name N or name CA or \ name C or name O or name CB )) or resid 512 through 585 or resid 587 through 637 \ or (resid 638 and (name N or name CA or name C or name O or name CB )) or resid \ 639 or resid 641 through 650 or resid 653 through 655 or (resid 656 and (name N \ or name CA or name C or name O or name CB )) or resid 657 through 660 or (resid \ 661 and (name N or name CA or name C or name O or name CB )) or resid 662 or (r \ esid 663 and (name N or name CA or name C or name O or name CB )) or resid 664 t \ hrough 667 or resid 669 or (resid 670 and (name N or name CA or name C or name O \ or name CB )) or resid 671 through 673 or (resid 674 and (name N or name CA or \ name C or name O or name CB )) or resid 676 through 686 or resid 688 through 689 \ or resid 692 through 698 or (resid 699 and (name N or name CA or name C or name \ O or name CB )) or resid 700 through 704 or (resid 705 and (name N or name CA o \ r name C or name O or name CB )) or resid 706 through 715 or (resid 716 and (nam \ e N or name CA or name C or name O or name CB )) or resid 717 through 740 or res \ id 742 or resid 745 through 763 or resid 765 through 774 or resid 776 through 77 \ 7 or resid 783 through 799 or resid 801 through 817 or (resid 818 through 819 an \ d (name N or name CA or name C or name O or name CB )) or resid 901 through 903) \ ) selection = (chain 'C' and (resid 393 through 398 or resid 400 through 403 or resid 405 thro \ ugh 406 or (resid 407 and (name N or name CA or name C or name O or name CB )) o \ r resid 412 through 414 or resid 416 through 422 or resid 424 through 431 or res \ id 433 or resid 436 or resid 438 or resid 440 through 441 or resid 443 through 4 \ 49 or (resid 450 and (name N or name CA or name C or name O or name CB )) or res \ id 452 through 453 or (resid 454 and (name N or name CA or name C or name O or n \ ame CB )) or resid 456 through 466 or resid 468 through 469 or resid 471 or resi \ d 473 through 546 or resid 567 through 581 or resid 583 through 635 or resid 637 \ through 646 or resid 649 through 663 or resid 665 through 670 or resid 672 thro \ ugh 682 or resid 684 through 685 or resid 688 through 692 or (resid 693 and (nam \ e N or name CA or name C or name O or name CB )) or resid 694 through 736 or res \ id 738 or resid 741 through 756 or (resid 757 and (name N or name CA or name C o \ r name O or name CB )) or resid 758 through 759 or resid 761 through 770 or (res \ id 772 through 773 and (name N or name CA or name C or name O or name CB )) or r \ esid 779 through 795 or resid 797 through 815 or resid 901 through 903)) selection = (chain 'D' and (resid 397 through 402 or resid 404 through 407 or resid 409 thro \ ugh 411 or resid 416 through 418 or resid 420 through 426 or resid 428 through 4 \ 35 or resid 437 or resid 440 or resid 442 or resid 444 through 445 or (resid 447 \ and (name N or name CA or name C or name O or name CB )) or resid 448 through 4 \ 54 or resid 456 through 458 or resid 460 through 470 or resid 472 through 473 or \ resid 475 or resid 477 through 508 or (resid 509 and (name N or name CA or name \ C or name O or name CB )) or resid 510 or (resid 511 and (name N or name CA or \ name C or name O or name CB )) or resid 512 through 585 or resid 587 through 637 \ or (resid 638 and (name N or name CA or name C or name O or name CB )) or resid \ 639 or resid 641 through 650 or resid 653 through 655 or (resid 656 and (name N \ or name CA or name C or name O or name CB )) or resid 657 through 660 or (resid \ 661 and (name N or name CA or name C or name O or name CB )) or resid 662 or (r \ esid 663 and (name N or name CA or name C or name O or name CB )) or resid 664 t \ hrough 667 or resid 669 or (resid 670 and (name N or name CA or name C or name O \ or name CB )) or resid 671 through 673 or (resid 674 and (name N or name CA or \ name C or name O or name CB )) or resid 676 through 686 or resid 688 through 689 \ or resid 692 through 698 or (resid 699 and (name N or name CA or name C or name \ O or name CB )) or resid 700 through 704 or (resid 705 and (name N or name CA o \ r name C or name O or name CB )) or resid 706 through 715 or (resid 716 and (nam \ e N or name CA or name C or name O or name CB )) or resid 717 through 740 or res \ id 742 or resid 745 through 763 or resid 765 through 774 or resid 776 through 77 \ 7 or resid 783 through 799 or resid 801 through 817 or (resid 818 through 819 an \ d (name N or name CA or name C or name O or name CB )) or resid 901 through 903) \ ) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.620 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: 7.430 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 44.440 Find NCS groups from input model: 0.990 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:10.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.280 16066 Z= 0.762 Angle : 1.214 26.695 21662 Z= 0.478 Chirality : 0.048 0.297 2404 Planarity : 0.004 0.104 2632 Dihedral : 16.279 163.853 5892 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.19), residues: 1966 helix: 1.88 (0.16), residues: 1056 sheet: -1.72 (0.37), residues: 178 loop : -0.95 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 667 HIS 0.008 0.002 HIS I 83 PHE 0.016 0.002 PHE I 205 TYR 0.015 0.002 TYR D 647 ARG 0.016 0.001 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 1.704 Fit side-chains REVERT: B 634 GLU cc_start: 0.7131 (pt0) cc_final: 0.6918 (pp20) REVERT: B 674 MET cc_start: 0.6113 (mtp) cc_final: 0.5896 (mtp) REVERT: A 389 ARG cc_start: 0.7045 (ptt90) cc_final: 0.6736 (ptt90) REVERT: A 436 TYR cc_start: 0.8197 (p90) cc_final: 0.7948 (p90) REVERT: A 459 MET cc_start: 0.7558 (mtm) cc_final: 0.7335 (mtm) REVERT: A 803 MET cc_start: 0.7859 (mtm) cc_final: 0.7647 (mtm) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 1.4741 time to fit residues: 369.9096 Evaluate side-chains 167 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.670 ------------------------------------------------------------------------------- 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: 1.9990 chunk 148 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 153 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 93 optimal weight: 0.1980 chunk 114 optimal weight: 0.5980 chunk 177 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 435 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16066 Z= 0.176 Angle : 0.498 6.898 21662 Z= 0.256 Chirality : 0.039 0.132 2404 Planarity : 0.004 0.045 2632 Dihedral : 14.239 164.239 2708 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.58 % Allowed : 7.11 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.19), residues: 1966 helix: 2.24 (0.16), residues: 1086 sheet: -1.62 (0.39), residues: 154 loop : -0.84 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 762 HIS 0.007 0.002 HIS J 83 PHE 0.012 0.001 PHE J 130 TYR 0.017 0.001 TYR A 434 ARG 0.005 0.000 ARG C 416 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 190 time to evaluate : 1.797 Fit side-chains REVERT: B 640 SER cc_start: 0.8158 (t) cc_final: 0.7886 (m) REVERT: B 714 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.6411 (mp10) REVERT: D 449 LYS cc_start: 0.5200 (ptmt) cc_final: 0.4747 (pttt) REVERT: D 549 TYR cc_start: 0.7267 (t80) cc_final: 0.6923 (t80) REVERT: C 438 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8282 (tp) REVERT: A 389 ARG cc_start: 0.7332 (ptt90) cc_final: 0.7072 (ptt90) REVERT: A 459 MET cc_start: 0.7685 (mtm) cc_final: 0.7417 (mtm) REVERT: A 752 GLN cc_start: 0.7190 (mt0) cc_final: 0.6936 (mt0) outliers start: 24 outliers final: 9 residues processed: 206 average time/residue: 1.1925 time to fit residues: 273.2023 Evaluate side-chains 175 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 164 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 714 GLN Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 682 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.0370 chunk 55 optimal weight: 0.8980 chunk 148 optimal weight: 3.9990 chunk 121 optimal weight: 0.1980 chunk 49 optimal weight: 1.9990 chunk 178 optimal weight: 0.0770 chunk 192 optimal weight: 0.4980 chunk 158 optimal weight: 7.9990 chunk 176 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 143 optimal weight: 0.9990 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16066 Z= 0.130 Angle : 0.437 6.302 21662 Z= 0.226 Chirality : 0.037 0.122 2404 Planarity : 0.003 0.038 2632 Dihedral : 12.848 159.844 2708 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.32 % Allowed : 10.00 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.53 (0.20), residues: 1966 helix: 2.53 (0.16), residues: 1088 sheet: -1.33 (0.42), residues: 132 loop : -0.87 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 667 HIS 0.006 0.001 HIS I 83 PHE 0.010 0.001 PHE D 495 TYR 0.021 0.001 TYR A 434 ARG 0.003 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 183 time to evaluate : 1.617 Fit side-chains REVERT: B 674 MET cc_start: 0.6762 (mtp) cc_final: 0.6516 (mtm) REVERT: B 714 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.6462 (mp10) REVERT: D 449 LYS cc_start: 0.4928 (ptmt) cc_final: 0.4579 (pttt) REVERT: D 473 ASP cc_start: 0.4850 (m-30) cc_final: 0.4555 (m-30) REVERT: D 549 TYR cc_start: 0.7309 (t80) cc_final: 0.6990 (t80) REVERT: C 438 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8389 (tp) REVERT: C 748 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7545 (ttpp) REVERT: A 389 ARG cc_start: 0.7182 (ptt90) cc_final: 0.6953 (ptt90) REVERT: A 459 MET cc_start: 0.7724 (mtm) cc_final: 0.7444 (mtm) REVERT: A 523 MET cc_start: 0.8791 (mmm) cc_final: 0.8494 (mmm) REVERT: A 752 GLN cc_start: 0.7213 (mt0) cc_final: 0.6994 (mt0) outliers start: 20 outliers final: 8 residues processed: 195 average time/residue: 1.2909 time to fit residues: 279.1316 Evaluate side-chains 173 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 162 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 714 GLN Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 594 ARG Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 748 LYS Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 662 VAL 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: 0.9990 chunk 92 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 chunk 189 optimal weight: 0.3980 chunk 93 optimal weight: 0.0770 chunk 169 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- 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: 0.7787 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16066 Z= 0.168 Angle : 0.465 8.625 21662 Z= 0.238 Chirality : 0.038 0.146 2404 Planarity : 0.003 0.038 2632 Dihedral : 12.337 150.840 2708 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.64 % Allowed : 11.25 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.42 (0.19), residues: 1966 helix: 2.44 (0.16), residues: 1086 sheet: -1.59 (0.40), residues: 142 loop : -0.85 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 667 HIS 0.005 0.001 HIS I 83 PHE 0.011 0.001 PHE I 130 TYR 0.019 0.001 TYR A 434 ARG 0.003 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 183 time to evaluate : 1.540 Fit side-chains REVERT: B 629 MET cc_start: 0.7323 (mpp) cc_final: 0.6918 (mtt) REVERT: B 674 MET cc_start: 0.6755 (mtp) cc_final: 0.6440 (mtm) REVERT: D 399 THR cc_start: 0.7200 (OUTLIER) cc_final: 0.6961 (m) REVERT: D 449 LYS cc_start: 0.5035 (ptmt) cc_final: 0.4617 (pttt) REVERT: D 473 ASP cc_start: 0.4832 (m-30) cc_final: 0.4532 (m-30) REVERT: C 438 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8419 (tp) REVERT: C 748 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7609 (ttpp) REVERT: A 389 ARG cc_start: 0.7183 (ptt90) cc_final: 0.6910 (ptt90) REVERT: A 679 VAL cc_start: 0.7400 (m) cc_final: 0.7153 (m) outliers start: 25 outliers final: 11 residues processed: 198 average time/residue: 1.1585 time to fit residues: 256.9056 Evaluate side-chains 181 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 167 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 594 ARG Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 748 LYS Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 662 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 141 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 47 optimal weight: 0.0270 overall best weight: 1.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 752 GLN A 752 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16066 Z= 0.326 Angle : 0.569 8.471 21662 Z= 0.293 Chirality : 0.042 0.192 2404 Planarity : 0.004 0.044 2632 Dihedral : 13.256 146.197 2708 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.76 % Allowed : 12.30 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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 (0.19), residues: 1966 helix: 1.90 (0.16), residues: 1082 sheet: -1.80 (0.36), residues: 180 loop : -0.94 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 574 HIS 0.005 0.001 HIS I 198 PHE 0.018 0.002 PHE I 130 TYR 0.018 0.002 TYR A 434 ARG 0.004 0.001 ARG B 599 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 178 time to evaluate : 1.698 Fit side-chains REVERT: B 629 MET cc_start: 0.7182 (OUTLIER) cc_final: 0.6851 (mtt) REVERT: B 770 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.7229 (ptmm) REVERT: D 399 THR cc_start: 0.7267 (OUTLIER) cc_final: 0.7009 (m) REVERT: D 473 ASP cc_start: 0.5099 (m-30) cc_final: 0.4602 (m-30) REVERT: D 721 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8434 (ptp) REVERT: D 747 ASN cc_start: 0.8342 (t0) cc_final: 0.7892 (t0) REVERT: D 762 LEU cc_start: 0.7868 (mt) cc_final: 0.7483 (mt) REVERT: C 438 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8431 (tp) REVERT: C 748 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7609 (ttpp) REVERT: A 647 GLU cc_start: 0.5462 (pm20) cc_final: 0.5152 (mp0) outliers start: 42 outliers final: 18 residues processed: 208 average time/residue: 1.1923 time to fit residues: 277.1240 Evaluate side-chains 190 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 166 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 770 LYS Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 594 ARG Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 630 GLU Chi-restraints excluded: chain C residue 658 SER Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 748 LYS Chi-restraints excluded: chain C residue 803 MET Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 807 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 3.9990 chunk 170 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 111 optimal weight: 0.0570 chunk 46 optimal weight: 0.0060 chunk 189 optimal weight: 0.0050 chunk 157 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 overall best weight: 0.3128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 752 GLN A 752 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16066 Z= 0.126 Angle : 0.439 9.085 21662 Z= 0.225 Chirality : 0.037 0.130 2404 Planarity : 0.003 0.040 2632 Dihedral : 11.722 125.029 2708 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.58 % Allowed : 14.74 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.35 (0.20), residues: 1966 helix: 2.41 (0.16), residues: 1084 sheet: -1.58 (0.36), residues: 178 loop : -0.88 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 667 HIS 0.005 0.001 HIS J 83 PHE 0.011 0.001 PHE D 495 TYR 0.018 0.001 TYR A 434 ARG 0.006 0.000 ARG A 467 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 189 time to evaluate : 1.921 Fit side-chains REVERT: B 629 MET cc_start: 0.7172 (mpp) cc_final: 0.6667 (mtt) REVERT: B 661 ARG cc_start: 0.7667 (mtm180) cc_final: 0.7427 (ptt90) REVERT: B 674 MET cc_start: 0.6795 (mtp) cc_final: 0.6520 (mtm) REVERT: I 48 ARG cc_start: 0.7447 (mtt-85) cc_final: 0.7173 (mtt90) REVERT: D 399 THR cc_start: 0.7205 (OUTLIER) cc_final: 0.6985 (m) REVERT: D 449 LYS cc_start: 0.4897 (ptmt) cc_final: 0.4499 (pttt) REVERT: D 473 ASP cc_start: 0.4851 (m-30) cc_final: 0.4578 (m-30) REVERT: D 629 MET cc_start: 0.7509 (mpp) cc_final: 0.7305 (mtp) REVERT: D 768 TYR cc_start: 0.5950 (m-10) cc_final: 0.5673 (m-10) REVERT: C 438 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8465 (tp) outliers start: 24 outliers final: 7 residues processed: 207 average time/residue: 1.1418 time to fit residues: 264.0717 Evaluate side-chains 178 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 169 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 630 GLU Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain A residue 662 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 108 optimal weight: 0.0070 chunk 138 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 188 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 752 GLN A 752 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16066 Z= 0.216 Angle : 0.486 7.388 21662 Z= 0.250 Chirality : 0.039 0.142 2404 Planarity : 0.003 0.040 2632 Dihedral : 11.766 111.157 2708 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.78 % Allowed : 15.53 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1966 helix: 2.21 (0.16), residues: 1086 sheet: -1.45 (0.39), residues: 154 loop : -1.02 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 667 HIS 0.004 0.001 HIS I 83 PHE 0.017 0.001 PHE D 682 TYR 0.015 0.001 TYR A 434 ARG 0.005 0.000 ARG A 467 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 180 time to evaluate : 1.891 Fit side-chains REVERT: B 629 MET cc_start: 0.7149 (mpp) cc_final: 0.6824 (mtt) REVERT: B 661 ARG cc_start: 0.7721 (mtm180) cc_final: 0.7453 (ptt90) REVERT: B 674 MET cc_start: 0.6727 (mtp) cc_final: 0.6444 (mtm) REVERT: I 48 ARG cc_start: 0.7513 (mtt-85) cc_final: 0.7248 (mtt90) REVERT: D 399 THR cc_start: 0.7299 (OUTLIER) cc_final: 0.7037 (m) REVERT: D 473 ASP cc_start: 0.5012 (m-30) cc_final: 0.4659 (m-30) REVERT: D 545 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.7280 (ttt-90) REVERT: D 762 LEU cc_start: 0.7848 (mt) cc_final: 0.7530 (mt) REVERT: D 768 TYR cc_start: 0.5928 (m-10) cc_final: 0.5648 (m-10) REVERT: C 438 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8361 (tp) REVERT: A 717 MET cc_start: 0.7536 (ptm) cc_final: 0.7126 (ptp) outliers start: 27 outliers final: 13 residues processed: 201 average time/residue: 1.1041 time to fit residues: 248.9562 Evaluate side-chains 189 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 173 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 545 ARG Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 594 ARG Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain A residue 662 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 112 optimal weight: 20.0000 chunk 56 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 128 optimal weight: 0.0980 chunk 93 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 148 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 752 GLN A 752 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16066 Z= 0.178 Angle : 0.476 11.613 21662 Z= 0.241 Chirality : 0.038 0.140 2404 Planarity : 0.003 0.040 2632 Dihedral : 11.240 104.864 2708 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.97 % Allowed : 15.66 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.19), residues: 1966 helix: 2.28 (0.16), residues: 1084 sheet: -1.41 (0.39), residues: 154 loop : -1.00 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 766 HIS 0.004 0.001 HIS I 83 PHE 0.010 0.001 PHE J 130 TYR 0.015 0.001 TYR A 434 ARG 0.004 0.000 ARG A 467 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 180 time to evaluate : 1.828 Fit side-chains REVERT: B 629 MET cc_start: 0.7133 (mpp) cc_final: 0.6653 (mtt) REVERT: B 661 ARG cc_start: 0.7758 (mtm180) cc_final: 0.7505 (ptt90) REVERT: B 674 MET cc_start: 0.6973 (mtp) cc_final: 0.6692 (mtm) REVERT: I 48 ARG cc_start: 0.7443 (mtt-85) cc_final: 0.7179 (mtt90) REVERT: D 399 THR cc_start: 0.7218 (OUTLIER) cc_final: 0.6954 (m) REVERT: D 473 ASP cc_start: 0.4944 (m-30) cc_final: 0.4619 (m-30) REVERT: D 629 MET cc_start: 0.7521 (mpp) cc_final: 0.7149 (mtt) REVERT: C 438 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8402 (tp) REVERT: C 748 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7533 (ttpp) REVERT: A 501 LYS cc_start: 0.6905 (tptt) cc_final: 0.6390 (mttt) outliers start: 30 outliers final: 12 residues processed: 203 average time/residue: 1.1450 time to fit residues: 262.6111 Evaluate side-chains 190 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 175 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 748 LYS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 662 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 0.4980 chunk 180 optimal weight: 0.2980 chunk 165 optimal weight: 0.1980 chunk 176 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 138 optimal weight: 1.9990 chunk 54 optimal weight: 0.0570 chunk 159 optimal weight: 0.6980 chunk 166 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 overall best weight: 0.3498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 752 GLN A 752 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16066 Z= 0.129 Angle : 0.445 8.909 21662 Z= 0.226 Chirality : 0.037 0.130 2404 Planarity : 0.003 0.040 2632 Dihedral : 10.351 98.023 2708 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.38 % Allowed : 16.64 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.42 (0.19), residues: 1966 helix: 2.48 (0.16), residues: 1084 sheet: -1.30 (0.39), residues: 154 loop : -0.97 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 766 HIS 0.005 0.001 HIS I 83 PHE 0.012 0.001 PHE D 682 TYR 0.015 0.001 TYR A 812 ARG 0.004 0.000 ARG A 467 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 187 time to evaluate : 1.697 Fit side-chains REVERT: B 629 MET cc_start: 0.7138 (mpp) cc_final: 0.6763 (mtt) REVERT: B 661 ARG cc_start: 0.7687 (mtm180) cc_final: 0.7484 (ptt90) REVERT: B 674 MET cc_start: 0.6698 (mtp) cc_final: 0.6390 (mtm) REVERT: D 399 THR cc_start: 0.7237 (OUTLIER) cc_final: 0.6938 (m) REVERT: D 434 LYS cc_start: 0.6898 (tmtt) cc_final: 0.6491 (ttpp) REVERT: D 473 ASP cc_start: 0.4907 (m-30) cc_final: 0.4645 (m-30) REVERT: D 629 MET cc_start: 0.7445 (mpp) cc_final: 0.7244 (mtp) REVERT: D 762 LEU cc_start: 0.7837 (mt) cc_final: 0.7499 (mt) REVERT: A 501 LYS cc_start: 0.6866 (tptt) cc_final: 0.6353 (mttt) REVERT: A 717 MET cc_start: 0.7671 (ptm) cc_final: 0.7351 (ptp) outliers start: 21 outliers final: 7 residues processed: 204 average time/residue: 1.1264 time to fit residues: 257.9627 Evaluate side-chains 179 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 171 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain A residue 662 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 2.9990 chunk 186 optimal weight: 0.9980 chunk 113 optimal weight: 0.4980 chunk 88 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 195 optimal weight: 0.9990 chunk 179 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 752 GLN A 752 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16066 Z= 0.191 Angle : 0.494 12.648 21662 Z= 0.249 Chirality : 0.038 0.131 2404 Planarity : 0.004 0.039 2632 Dihedral : 10.616 89.219 2708 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.86 % Allowed : 16.97 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.19), residues: 1966 helix: 2.31 (0.16), residues: 1084 sheet: -1.30 (0.39), residues: 154 loop : -1.00 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 766 HIS 0.004 0.001 HIS I 83 PHE 0.011 0.001 PHE C 542 TYR 0.015 0.001 TYR A 812 ARG 0.004 0.000 ARG A 467 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 177 time to evaluate : 1.579 Fit side-chains REVERT: B 629 MET cc_start: 0.7128 (mpp) cc_final: 0.6767 (mtt) REVERT: B 661 ARG cc_start: 0.7703 (mtm180) cc_final: 0.7485 (ptt90) REVERT: B 674 MET cc_start: 0.6590 (mtp) cc_final: 0.6289 (mtm) REVERT: D 399 THR cc_start: 0.7275 (OUTLIER) cc_final: 0.6951 (m) REVERT: D 434 LYS cc_start: 0.6897 (tmtt) cc_final: 0.6486 (ttpp) REVERT: D 473 ASP cc_start: 0.4887 (m-30) cc_final: 0.4647 (m-30) REVERT: A 501 LYS cc_start: 0.6882 (tptt) cc_final: 0.6392 (mttt) REVERT: A 626 VAL cc_start: 0.8330 (m) cc_final: 0.8080 (t) REVERT: A 717 MET cc_start: 0.7672 (ptm) cc_final: 0.7410 (ptm) outliers start: 13 outliers final: 8 residues processed: 187 average time/residue: 1.0887 time to fit residues: 229.5761 Evaluate side-chains 181 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 172 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain C residue 499 MET Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain A residue 662 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 1.9990 chunk 165 optimal weight: 0.0370 chunk 47 optimal weight: 20.0000 chunk 143 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 65 optimal weight: 20.0000 chunk 159 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 overall best weight: 1.1464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 752 GLN A 752 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.173678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.112812 restraints weight = 16702.563| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.06 r_work: 0.2933 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16066 Z= 0.251 Angle : 0.525 8.596 21662 Z= 0.268 Chirality : 0.040 0.149 2404 Planarity : 0.004 0.041 2632 Dihedral : 11.103 94.673 2708 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.18 % Allowed : 16.84 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.19), residues: 1966 helix: 2.08 (0.16), residues: 1084 sheet: -1.37 (0.39), residues: 160 loop : -1.05 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 766 HIS 0.004 0.001 HIS I 198 PHE 0.014 0.001 PHE J 130 TYR 0.017 0.002 TYR A 812 ARG 0.004 0.000 ARG A 467 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5317.83 seconds wall clock time: 95 minutes 24.77 seconds (5724.77 seconds total)