Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 9 18:25:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnn_26015/10_2023/7tnn_26015_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnn_26015/10_2023/7tnn_26015.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnn_26015/10_2023/7tnn_26015.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnn_26015/10_2023/7tnn_26015.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnn_26015/10_2023/7tnn_26015_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnn_26015/10_2023/7tnn_26015_updated.pdb" } resolution = 3.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 136 5.16 5 Cl 4 4.86 5 C 12564 2.51 5 N 3144 2.21 5 O 3591 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 453": "NH1" <-> "NH2" Residue "A PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A ARG 628": "NH1" <-> "NH2" Residue "A TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 684": "NH1" <-> "NH2" Residue "A ARG 819": "NH1" <-> "NH2" Residue "A ARG 1036": "NH1" <-> "NH2" Residue "B PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 453": "NH1" <-> "NH2" Residue "B PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 545": "NH1" <-> "NH2" Residue "B PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 684": "NH1" <-> "NH2" Residue "B ARG 819": "NH1" <-> "NH2" Residue "B ARG 1036": "NH1" <-> "NH2" Residue "B PHE 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1203": "NH1" <-> "NH2" Residue "C PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 545": "NH1" <-> "NH2" Residue "C TYR 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 599": "NH1" <-> "NH2" Residue "C ARG 628": "NH1" <-> "NH2" Residue "C ARG 819": "NH1" <-> "NH2" Residue "C ARG 1036": "NH1" <-> "NH2" Residue "D PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 545": "NH1" <-> "NH2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1036": "NH1" <-> "NH2" Residue "D ARG 1203": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 19439 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 4816 Classifications: {'peptide': 619} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 602} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4828 Classifications: {'peptide': 621} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 604} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 4854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 4854 Classifications: {'peptide': 624} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 607} Chain breaks: 2 Chain: "D" Number of atoms: 4825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4825 Classifications: {'peptide': 620} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 603} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'CYZ': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'CYZ': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.09, per 1000 atoms: 0.52 Number of scatterers: 19439 At special positions: 0 Unit cell: (126.16, 115.37, 137.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 136 16.00 O 3591 8.00 N 3144 7.00 C 12564 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.04 Simple disulfide: pdb=" SG CYS A1039 " - pdb=" SG CYS A1067 " distance=2.03 Simple disulfide: pdb=" SG CYS A1066 " - pdb=" SG CYS A1076 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.04 Simple disulfide: pdb=" SG CYS B1039 " - pdb=" SG CYS B1067 " distance=2.04 Simple disulfide: pdb=" SG CYS B1066 " - pdb=" SG CYS B1076 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.02 Simple disulfide: pdb=" SG CYS C1039 " - pdb=" SG CYS C1067 " distance=2.03 Simple disulfide: pdb=" SG CYS C1066 " - pdb=" SG CYS C1076 " distance=2.04 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.02 Simple disulfide: pdb=" SG CYS D1039 " - pdb=" SG CYS D1067 " distance=2.03 Simple disulfide: pdb=" SG CYS D1066 " - pdb=" SG CYS D1076 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.22 Conformation dependent library (CDL) restraints added in 3.3 seconds 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4552 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 98 helices and 21 sheets defined 50.5% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.44 Creating SS restraints... Processing helix chain 'A' and resid 417 through 420 Processing helix chain 'A' and resid 424 through 436 Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 483 through 488 removed outlier: 3.945A pdb=" N VAL A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 518 No H-bonds generated for 'chain 'A' and resid 516 through 518' Processing helix chain 'A' and resid 523 through 544 removed outlier: 3.508A pdb=" N SER A 537 " --> pdb=" O TYR A 533 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 584 Processing helix chain 'A' and resid 596 through 624 removed outlier: 3.570A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 640 Processing helix chain 'A' and resid 654 through 660 Processing helix chain 'A' and resid 665 through 675 Processing helix chain 'A' and resid 686 through 696 Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 743 through 756 Processing helix chain 'A' and resid 758 through 769 Processing helix chain 'A' and resid 789 through 791 No H-bonds generated for 'chain 'A' and resid 789 through 791' Processing helix chain 'A' and resid 793 through 819 Processing helix chain 'A' and resid 1005 through 1028 Processing helix chain 'A' and resid 1051 through 1055 Processing helix chain 'A' and resid 1092 through 1103 Processing helix chain 'A' and resid 1105 through 1125 Processing helix chain 'A' and resid 1133 through 1160 Processing helix chain 'A' and resid 1177 through 1206 Processing helix chain 'B' and resid 417 through 420 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 488 removed outlier: 3.661A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 519 Processing helix chain 'B' and resid 523 through 544 Processing helix chain 'B' and resid 566 through 568 No H-bonds generated for 'chain 'B' and resid 566 through 568' Processing helix chain 'B' and resid 573 through 584 Processing helix chain 'B' and resid 599 through 616 Processing helix chain 'B' and resid 620 through 625 Processing helix chain 'B' and resid 636 through 640 Processing helix chain 'B' and resid 654 through 660 Processing helix chain 'B' and resid 665 through 675 Processing helix chain 'B' and resid 686 through 695 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 742 through 755 Processing helix chain 'B' and resid 758 through 769 Processing helix chain 'B' and resid 774 through 777 No H-bonds generated for 'chain 'B' and resid 774 through 777' Processing helix chain 'B' and resid 794 through 818 Processing helix chain 'B' and resid 1005 through 1028 Processing helix chain 'B' and resid 1051 through 1055 removed outlier: 3.694A pdb=" N GLU B1055 " --> pdb=" O LYS B1052 " (cutoff:3.500A) Processing helix chain 'B' and resid 1092 through 1103 Processing helix chain 'B' and resid 1105 through 1123 Processing helix chain 'B' and resid 1133 through 1160 removed outlier: 3.565A pdb=" N ALA B1160 " --> pdb=" O ILE B1156 " (cutoff:3.500A) Processing helix chain 'B' and resid 1177 through 1208 Processing helix chain 'C' and resid 410 through 412 No H-bonds generated for 'chain 'C' and resid 410 through 412' Processing helix chain 'C' and resid 417 through 420 Processing helix chain 'C' and resid 424 through 436 Processing helix chain 'C' and resid 463 through 468 Processing helix chain 'C' and resid 483 through 486 No H-bonds generated for 'chain 'C' and resid 483 through 486' Processing helix chain 'C' and resid 516 through 518 No H-bonds generated for 'chain 'C' and resid 516 through 518' Processing helix chain 'C' and resid 523 through 544 Processing helix chain 'C' and resid 566 through 568 No H-bonds generated for 'chain 'C' and resid 566 through 568' Processing helix chain 'C' and resid 573 through 584 Processing helix chain 'C' and resid 596 through 624 removed outlier: 3.530A pdb=" N ILE C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 641 Processing helix chain 'C' and resid 654 through 660 Processing helix chain 'C' and resid 665 through 675 removed outlier: 3.642A pdb=" N TYR C 673 " --> pdb=" O LYS C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 695 Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 743 through 755 removed outlier: 3.563A pdb=" N LEU C 751 " --> pdb=" O ASN C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 768 Processing helix chain 'C' and resid 790 through 821 removed outlier: 3.527A pdb=" N ALA C 793 " --> pdb=" O SER C 790 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N GLY C 794 " --> pdb=" O ASN C 791 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR C 797 " --> pdb=" O GLY C 794 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL C 800 " --> pdb=" O TYR C 797 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET C 807 " --> pdb=" O GLY C 804 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU C 811 " --> pdb=" O LEU C 808 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS C 817 " --> pdb=" O PHE C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1028 Processing helix chain 'C' and resid 1040 through 1042 No H-bonds generated for 'chain 'C' and resid 1040 through 1042' Processing helix chain 'C' and resid 1051 through 1053 No H-bonds generated for 'chain 'C' and resid 1051 through 1053' Processing helix chain 'C' and resid 1092 through 1103 Processing helix chain 'C' and resid 1105 through 1124 removed outlier: 3.506A pdb=" N SER C1124 " --> pdb=" O CYS C1120 " (cutoff:3.500A) Processing helix chain 'C' and resid 1133 through 1159 Processing helix chain 'C' and resid 1177 through 1208 removed outlier: 3.528A pdb=" N GLN C1206 " --> pdb=" O ASP C1202 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 420 Processing helix chain 'D' and resid 424 through 436 removed outlier: 3.596A 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 488 removed outlier: 3.686A pdb=" N VAL D 488 " --> pdb=" O VAL D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 519 Processing helix chain 'D' and resid 523 through 544 Processing helix chain 'D' and resid 566 through 568 No H-bonds generated for 'chain 'D' and resid 566 through 568' Processing helix chain 'D' and resid 573 through 584 Processing helix chain 'D' and resid 596 through 617 Processing helix chain 'D' and resid 620 through 625 Processing helix chain 'D' and resid 636 through 640 Processing helix chain 'D' and resid 654 through 660 removed outlier: 3.517A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 676 removed outlier: 3.574A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 695 Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 758 through 768 Processing helix chain 'D' and resid 774 through 777 No H-bonds generated for 'chain 'D' and resid 774 through 777' Processing helix chain 'D' and resid 794 through 820 Processing helix chain 'D' and resid 1005 through 1028 Processing helix chain 'D' and resid 1049 through 1051 No H-bonds generated for 'chain 'D' and resid 1049 through 1051' Processing helix chain 'D' and resid 1093 through 1102 Processing helix chain 'D' and resid 1105 through 1124 Processing helix chain 'D' and resid 1132 through 1159 Processing helix chain 'D' and resid 1177 through 1206 removed outlier: 3.609A pdb=" N HIS D1204 " --> pdb=" O PHE D1200 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 395 through 399 Processing sheet with id= B, first strand: chain 'A' and resid 489 through 491 Processing sheet with id= C, first strand: chain 'A' and resid 720 through 723 removed outlier: 3.874A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.057A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1033 through 1036 removed outlier: 3.851A pdb=" N CYS A1066 " --> pdb=" O HIS A1059 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 494 through 498 removed outlier: 6.940A pdb=" N TYR A 732 " --> pdb=" O PHE A 495 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N SER A 497 " --> pdb=" O LYS A 730 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LYS A 730 " --> pdb=" O SER A 497 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 395 through 399 Processing sheet with id= G, first strand: chain 'B' and resid 496 through 499 removed outlier: 3.613A 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: 3.573A pdb=" N VAL B 723 " --> pdb=" O ILE B 502 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.088A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 1033 through 1036 Processing sheet with id= J, first strand: chain 'B' and resid 1064 through 1066 Processing sheet with id= K, first strand: chain 'C' and resid 395 through 399 Processing sheet with id= L, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.598A pdb=" N ALA C 452 " --> pdb=" O ASN C 461 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE C 459 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 489 through 491 Processing sheet with id= N, first strand: chain 'C' and resid 720 through 723 removed outlier: 3.822A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.426A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 1033 through 1036 Processing sheet with id= P, first strand: chain 'C' and resid 494 through 498 removed outlier: 6.785A pdb=" N TYR C 732 " --> pdb=" O PHE C 495 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N SER C 497 " --> pdb=" O LYS C 730 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LYS C 730 " --> pdb=" O SER C 497 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 395 through 399 Processing sheet with id= R, first strand: chain 'D' and resid 489 through 491 Processing sheet with id= S, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.669A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 720 through 723 removed outlier: 3.727A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 1033 through 1037 removed outlier: 3.748A pdb=" N VAL D1056 " --> pdb=" O GLY D1037 " (cutoff:3.500A) 942 hydrogen bonds defined for protein. 2718 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: 5.78 Time building geometry restraints manager: 7.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5955 1.34 - 1.47: 5182 1.47 - 1.60: 8507 1.60 - 1.72: 11 1.72 - 1.85: 217 Bond restraints: 19872 Sorted by residual: bond pdb=" CA ARG D 675 " pdb=" C ARG D 675 " ideal model delta sigma weight residual 1.522 1.565 -0.043 1.37e-02 5.33e+03 9.66e+00 bond pdb=" CG LEU A 704 " pdb=" CD1 LEU A 704 " ideal model delta sigma weight residual 1.521 1.436 0.085 3.30e-02 9.18e+02 6.59e+00 bond pdb=" N3 CYZ D1301 " pdb=" S2 CYZ D1301 " ideal model delta sigma weight residual 1.644 1.601 0.043 2.00e-02 2.50e+03 4.56e+00 bond pdb=" N3 CYZ A1302 " pdb=" S2 CYZ A1302 " ideal model delta sigma weight residual 1.644 1.602 0.042 2.00e-02 2.50e+03 4.40e+00 bond pdb=" N3 CYZ B1302 " pdb=" S2 CYZ B1302 " ideal model delta sigma weight residual 1.644 1.602 0.042 2.00e-02 2.50e+03 4.35e+00 ... (remaining 19867 not shown) Histogram of bond angle deviations from ideal: 93.20 - 101.39: 91 101.39 - 109.58: 1932 109.58 - 117.78: 12810 117.78 - 125.97: 11701 125.97 - 134.16: 317 Bond angle restraints: 26851 Sorted by residual: angle pdb=" C LEU B 596 " pdb=" N SER B 597 " pdb=" CA SER B 597 " ideal model delta sigma weight residual 121.54 130.98 -9.44 1.91e+00 2.74e-01 2.44e+01 angle pdb=" C ALA C 775 " pdb=" N LYS C 776 " pdb=" CA LYS C 776 " ideal model delta sigma weight residual 121.54 130.81 -9.27 1.91e+00 2.74e-01 2.35e+01 angle pdb=" C THR D 784 " pdb=" N SER D 785 " pdb=" CA SER D 785 " ideal model delta sigma weight residual 121.31 128.47 -7.16 1.49e+00 4.50e-01 2.31e+01 angle pdb=" N SER D 785 " pdb=" CA SER D 785 " pdb=" C SER D 785 " ideal model delta sigma weight residual 110.35 116.87 -6.52 1.40e+00 5.10e-01 2.17e+01 angle pdb=" N ARG C 628 " pdb=" CA ARG C 628 " pdb=" CB ARG C 628 " ideal model delta sigma weight residual 110.49 102.74 7.75 1.69e+00 3.50e-01 2.10e+01 ... (remaining 26846 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.24: 11215 19.24 - 38.48: 422 38.48 - 57.72: 52 57.72 - 76.96: 10 76.96 - 96.20: 6 Dihedral angle restraints: 11705 sinusoidal: 4570 harmonic: 7135 Sorted by residual: dihedral pdb=" CA GLU C 627 " pdb=" C GLU C 627 " pdb=" N ARG C 628 " pdb=" CA ARG C 628 " ideal model delta harmonic sigma weight residual -180.00 -133.20 -46.80 0 5.00e+00 4.00e-02 8.76e+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 -86.00 -168.23 82.23 1 1.00e+01 1.00e-02 8.30e+01 dihedral pdb=" CB CYS D1039 " pdb=" SG CYS D1039 " pdb=" SG CYS D1067 " pdb=" CB CYS D1067 " ideal model delta sinusoidal sigma weight residual 93.00 26.80 66.20 1 1.00e+01 1.00e-02 5.73e+01 ... (remaining 11702 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2439 0.066 - 0.132: 463 0.132 - 0.198: 77 0.198 - 0.264: 17 0.264 - 0.330: 2 Chirality restraints: 2998 Sorted by residual: chirality pdb=" CG LEU D 639 " pdb=" CB LEU D 639 " pdb=" CD1 LEU D 639 " pdb=" CD2 LEU D 639 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CB ILE B 476 " pdb=" CA ILE B 476 " pdb=" CG1 ILE B 476 " pdb=" CG2 ILE B 476 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" C8 CYZ C1301 " pdb=" C1 CYZ C1301 " pdb=" N1 CYZ C1301 " pdb=" N2 CYZ C1301 " both_signs ideal model delta sigma weight residual False 2.20 2.47 -0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 2995 not shown) Planarity restraints: 3313 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 627 " 0.017 2.00e-02 2.50e+03 3.46e-02 1.19e+01 pdb=" C GLU C 627 " -0.060 2.00e-02 2.50e+03 pdb=" O GLU C 627 " 0.022 2.00e-02 2.50e+03 pdb=" N ARG C 628 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 783 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.47e+00 pdb=" C LYS A 783 " -0.040 2.00e-02 2.50e+03 pdb=" O LYS A 783 " 0.015 2.00e-02 2.50e+03 pdb=" N THR A 784 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 511 " 0.012 2.00e-02 2.50e+03 2.30e-02 5.31e+00 pdb=" C LYS A 511 " -0.040 2.00e-02 2.50e+03 pdb=" O LYS A 511 " 0.015 2.00e-02 2.50e+03 pdb=" N PRO A 512 " 0.013 2.00e-02 2.50e+03 ... (remaining 3310 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4459 2.79 - 3.31: 18689 3.31 - 3.84: 31914 3.84 - 4.37: 36917 4.37 - 4.90: 63259 Nonbonded interactions: 155238 Sorted by model distance: nonbonded pdb=" OG SER C 597 " pdb=" O ALA D 806 " model vdw 2.257 2.440 nonbonded pdb=" OE1 GLU C 402 " pdb=" OH TYR C 450 " model vdw 2.273 2.440 nonbonded pdb=" O GLN D 642 " pdb=" OH TYR D 647 " model vdw 2.276 2.440 nonbonded pdb=" OG SER A 631 " pdb=" O ILE A 633 " model vdw 2.282 2.440 nonbonded pdb=" OE1 GLU D 402 " pdb=" OH TYR D 450 " model vdw 2.285 2.440 ... (remaining 155233 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 394 through 548 or (resid 549 and (name N or name CA or na \ me C or name O or name CB )) or resid 564 through 819 or resid 1002 through 1207 \ or resid 1302)) selection = (chain 'B' and (resid 394 through 549 or resid 564 through 626 or (resid 627 and \ (name N or name CA or name C or name O or name CB )) or resid 628 through 1207 \ or resid 1302)) selection = (chain 'C' and (resid 394 through 548 or (resid 549 and (name N or name CA or na \ me C or name O or name CB )) or resid 564 through 626 or (resid 627 and (name N \ or name CA or name C or name O or name CB )) or resid 628 through 819 or resid 1 \ 002 through 1207 or resid 1301)) selection = (chain 'D' and (resid 394 through 548 or (resid 549 and (name N or name CA or na \ me C or name O or name CB )) or resid 564 through 626 or (resid 627 and (name N \ or name CA or name C or name O or name CB )) or resid 628 through 819 or resid 1 \ 002 through 1207 or resid 1301)) } 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.570 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 48.860 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 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 : 0.005 0.085 19872 Z= 0.337 Angle : 0.919 15.267 26851 Z= 0.506 Chirality : 0.056 0.330 2998 Planarity : 0.006 0.053 3313 Dihedral : 10.688 96.196 7117 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.85 % Favored : 97.07 % Rotamer: Outliers : 0.34 % Allowed : 4.08 % Favored : 95.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.09 (0.13), residues: 2460 helix: -1.12 (0.10), residues: 1345 sheet: -0.28 (0.40), residues: 144 loop : -1.79 (0.17), residues: 971 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 690 time to evaluate : 2.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 694 average time/residue: 0.3169 time to fit residues: 332.1443 Evaluate side-chains 370 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 369 time to evaluate : 2.192 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1705 time to fit residues: 3.3383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 208 optimal weight: 6.9990 chunk 187 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 193 optimal weight: 0.4980 chunk 74 optimal weight: 0.6980 chunk 117 optimal weight: 0.7980 chunk 144 optimal weight: 0.9980 chunk 224 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1053 ASN A1204 HIS B 747 ASN B1008 GLN B1071 ASN ** B1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS C 586 GLN C 642 GLN C 714 GLN C 726 ASN C 791 ASN C1204 HIS D 411 ASN D 412 HIS D 714 GLN D1008 GLN ** D1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1171 ASN D1198 HIS D1204 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19872 Z= 0.191 Angle : 0.589 9.217 26851 Z= 0.315 Chirality : 0.041 0.192 2998 Planarity : 0.005 0.061 3313 Dihedral : 6.174 93.801 2693 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.35 % Allowed : 14.44 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.06 (0.16), residues: 2460 helix: 1.04 (0.13), residues: 1357 sheet: -0.45 (0.38), residues: 171 loop : -1.58 (0.18), residues: 932 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 412 time to evaluate : 2.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 27 residues processed: 442 average time/residue: 0.2658 time to fit residues: 187.8489 Evaluate side-chains 358 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 331 time to evaluate : 2.187 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1875 time to fit residues: 12.5176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 124 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 186 optimal weight: 0.0010 chunk 152 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 224 optimal weight: 0.9980 chunk 242 optimal weight: 7.9990 chunk 200 optimal weight: 0.7980 chunk 222 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 overall best weight: 1.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 791 ASN B1131 HIS ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 714 GLN C1053 ASN ** C1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1204 HIS D 714 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19872 Z= 0.202 Angle : 0.564 10.517 26851 Z= 0.295 Chirality : 0.040 0.215 2998 Planarity : 0.004 0.054 3313 Dihedral : 5.900 92.682 2693 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.49 % Allowed : 15.06 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.50 (0.16), residues: 2460 helix: 1.64 (0.14), residues: 1360 sheet: -0.59 (0.38), residues: 164 loop : -1.50 (0.19), residues: 936 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 366 time to evaluate : 2.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 33 residues processed: 397 average time/residue: 0.2626 time to fit residues: 168.8446 Evaluate side-chains 361 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 328 time to evaluate : 2.106 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.1734 time to fit residues: 13.6250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 222 optimal weight: 6.9990 chunk 168 optimal weight: 9.9990 chunk 116 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 chunk 225 optimal weight: 6.9990 chunk 238 optimal weight: 9.9990 chunk 117 optimal weight: 2.9990 chunk 213 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1204 HIS B1204 HIS ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1204 HIS D 714 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 19872 Z= 0.424 Angle : 0.681 8.075 26851 Z= 0.360 Chirality : 0.045 0.172 2998 Planarity : 0.005 0.052 3313 Dihedral : 6.314 95.057 2693 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.88 % Allowed : 17.12 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.06 (0.16), residues: 2460 helix: 1.28 (0.14), residues: 1352 sheet: -0.87 (0.36), residues: 175 loop : -1.67 (0.19), residues: 933 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 335 time to evaluate : 2.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 49 residues processed: 383 average time/residue: 0.2705 time to fit residues: 165.7704 Evaluate side-chains 349 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 300 time to evaluate : 1.954 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.1703 time to fit residues: 18.5263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 198 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 177 optimal weight: 10.0000 chunk 98 optimal weight: 0.0060 chunk 203 optimal weight: 0.0980 chunk 165 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 121 optimal weight: 0.8980 chunk 214 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 HIS C 709 ASN C1078 GLN C1204 HIS D 586 GLN D 714 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 19872 Z= 0.160 Angle : 0.565 11.952 26851 Z= 0.290 Chirality : 0.040 0.220 2998 Planarity : 0.003 0.042 3313 Dihedral : 5.882 91.789 2693 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.73 % Allowed : 17.94 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.53 (0.17), residues: 2460 helix: 1.72 (0.14), residues: 1360 sheet: -0.70 (0.39), residues: 151 loop : -1.56 (0.19), residues: 949 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 365 time to evaluate : 2.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 17 residues processed: 385 average time/residue: 0.2743 time to fit residues: 169.6608 Evaluate side-chains 329 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 312 time to evaluate : 2.132 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1930 time to fit residues: 8.8974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 80 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 238 optimal weight: 9.9990 chunk 198 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 79 optimal weight: 0.0370 chunk 125 optimal weight: 0.4980 overall best weight: 2.1064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 ASN A1204 HIS D 714 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 19872 Z= 0.283 Angle : 0.600 8.769 26851 Z= 0.311 Chirality : 0.041 0.190 2998 Planarity : 0.004 0.041 3313 Dihedral : 5.953 92.975 2693 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.77 % Allowed : 19.86 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.17), residues: 2460 helix: 1.61 (0.14), residues: 1361 sheet: -0.84 (0.39), residues: 152 loop : -1.65 (0.19), residues: 947 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 328 time to evaluate : 2.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 24 residues processed: 348 average time/residue: 0.2993 time to fit residues: 167.8723 Evaluate side-chains 331 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 307 time to evaluate : 2.135 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1869 time to fit residues: 11.3524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 230 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 174 optimal weight: 8.9990 chunk 135 optimal weight: 1.9990 chunk 201 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 238 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 145 optimal weight: 0.5980 chunk 109 optimal weight: 0.6980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 ASN ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1053 ASN A1204 HIS ** B1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1008 GLN C1204 HIS D 714 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19872 Z= 0.204 Angle : 0.568 8.774 26851 Z= 0.294 Chirality : 0.040 0.175 2998 Planarity : 0.003 0.040 3313 Dihedral : 5.877 92.080 2693 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.15 % Allowed : 20.58 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.48 (0.17), residues: 2460 helix: 1.74 (0.14), residues: 1354 sheet: -0.73 (0.39), residues: 163 loop : -1.68 (0.19), residues: 943 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 340 time to evaluate : 2.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 8 residues processed: 354 average time/residue: 0.2770 time to fit residues: 156.8509 Evaluate side-chains 322 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 314 time to evaluate : 1.951 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2045 time to fit residues: 5.6235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 147 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 22 optimal weight: 0.0020 chunk 187 optimal weight: 6.9990 chunk 216 optimal weight: 1.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 ASN ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1204 HIS B 587 GLN ** B1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1204 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19872 Z= 0.180 Angle : 0.563 9.582 26851 Z= 0.291 Chirality : 0.041 0.341 2998 Planarity : 0.003 0.040 3313 Dihedral : 5.736 91.603 2693 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.67 % Allowed : 21.44 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.57 (0.17), residues: 2460 helix: 1.81 (0.14), residues: 1359 sheet: -0.92 (0.39), residues: 167 loop : -1.60 (0.19), residues: 934 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 333 time to evaluate : 2.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 340 average time/residue: 0.2864 time to fit residues: 155.3979 Evaluate side-chains 317 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 310 time to evaluate : 2.151 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1837 time to fit residues: 5.3095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 228 optimal weight: 5.9990 chunk 208 optimal weight: 7.9990 chunk 221 optimal weight: 0.6980 chunk 133 optimal weight: 4.9990 chunk 96 optimal weight: 0.0670 chunk 174 optimal weight: 9.9990 chunk 68 optimal weight: 0.9990 chunk 200 optimal weight: 0.0070 chunk 209 optimal weight: 7.9990 chunk 145 optimal weight: 9.9990 chunk 234 optimal weight: 0.7980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 ASN ** B1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1204 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19872 Z= 0.154 Angle : 0.566 10.586 26851 Z= 0.289 Chirality : 0.040 0.267 2998 Planarity : 0.003 0.040 3313 Dihedral : 5.625 91.193 2693 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.43 % Allowed : 21.44 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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 (0.17), residues: 2460 helix: 1.94 (0.14), residues: 1354 sheet: -0.90 (0.38), residues: 168 loop : -1.57 (0.19), residues: 938 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 339 time to evaluate : 2.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 344 average time/residue: 0.3121 time to fit residues: 170.9866 Evaluate side-chains 318 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 315 time to evaluate : 2.823 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1933 time to fit residues: 3.3432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 143 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 163 optimal weight: 0.0070 chunk 246 optimal weight: 4.9990 chunk 226 optimal weight: 0.1980 chunk 195 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 151 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 208 optimal weight: 7.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 ASN B 587 GLN B 756 GLN ** B1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1204 HIS ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19872 Z= 0.158 Angle : 0.572 13.960 26851 Z= 0.290 Chirality : 0.040 0.264 2998 Planarity : 0.003 0.041 3313 Dihedral : 5.549 91.031 2693 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.72 % Allowed : 21.53 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.74 (0.17), residues: 2460 helix: 1.95 (0.14), residues: 1354 sheet: -0.78 (0.39), residues: 168 loop : -1.53 (0.19), residues: 938 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 326 time to evaluate : 2.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 333 average time/residue: 0.2804 time to fit residues: 151.1149 Evaluate side-chains 322 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 313 time to evaluate : 2.164 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1858 time to fit residues: 6.3188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 60 optimal weight: 0.6980 chunk 180 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 54 optimal weight: 0.7980 chunk 196 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 36 optimal weight: 0.0030 chunk 172 optimal weight: 0.3980 chunk 11 optimal weight: 7.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 ASN B 709 ASN ** B1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1204 HIS ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1204 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.128796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.103883 restraints weight = 38173.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.105184 restraints weight = 24089.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.105631 restraints weight = 17660.686| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19872 Z= 0.166 Angle : 0.581 13.936 26851 Z= 0.295 Chirality : 0.040 0.246 2998 Planarity : 0.003 0.041 3313 Dihedral : 5.515 90.752 2693 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.38 % Allowed : 22.11 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.74 (0.17), residues: 2460 helix: 1.96 (0.14), residues: 1354 sheet: -0.71 (0.38), residues: 175 loop : -1.55 (0.19), residues: 931 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4072.67 seconds wall clock time: 78 minutes 7.36 seconds (4687.36 seconds total)