Starting phenix.real_space_refine on Sat Feb 17 17:47:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnn_26015/02_2024/7tnn_26015_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnn_26015/02_2024/7tnn_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_26015/02_2024/7tnn_26015.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnn_26015/02_2024/7tnn_26015.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnn_26015/02_2024/7tnn_26015_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnn_26015/02_2024/7tnn_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-dev-5238/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: 10.56, per 1000 atoms: 0.54 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: 7.97 Conformation dependent library (CDL) restraints added in 3.7 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: 4.31 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: 6.05 Time building geometry restraints manager: 8.50 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 - 24.59: 11427 24.59 - 49.18: 337 49.18 - 73.78: 16 73.78 - 98.37: 13 98.37 - 122.96: 8 Dihedral angle restraints: 11801 sinusoidal: 4666 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 11798 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: 1.660 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: 7.660 Check model and map are aligned: 0.320 Set scattering table: 0.190 Process input model: 53.220 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.550 ------------------------------------------------------------------------------- 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 : 11.690 122.960 7213 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B1032 HIS 0.009 0.002 HIS C1081 PHE 0.028 0.003 PHE B 495 TYR 0.032 0.002 TYR A 702 ARG 0.007 0.001 ARG A 599 *********************** 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 : 2.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 CYS cc_start: 0.8872 (m) cc_final: 0.8576 (m) REVERT: A 498 LEU cc_start: 0.9339 (pp) cc_final: 0.8793 (pp) REVERT: A 516 SER cc_start: 0.8787 (p) cc_final: 0.8454 (t) REVERT: A 592 SER cc_start: 0.8394 (m) cc_final: 0.7996 (p) REVERT: A 634 GLU cc_start: 0.8103 (pt0) cc_final: 0.7402 (tp30) REVERT: A 661 ARG cc_start: 0.8043 (ptp-110) cc_final: 0.7819 (mtt-85) REVERT: A 708 MET cc_start: 0.7054 (mtt) cc_final: 0.6319 (mtt) REVERT: A 710 GLU cc_start: 0.7801 (tt0) cc_final: 0.7518 (mt-10) REVERT: A 1025 ILE cc_start: 0.8723 (mt) cc_final: 0.8498 (mt) REVERT: A 1033 LEU cc_start: 0.8326 (tt) cc_final: 0.8029 (pp) REVERT: A 1063 TRP cc_start: 0.6092 (m-10) cc_final: 0.5772 (m100) REVERT: A 1127 TYR cc_start: 0.6530 (m-10) cc_final: 0.6277 (m-10) REVERT: A 1171 ASN cc_start: 0.4647 (p0) cc_final: 0.4238 (t0) REVERT: B 438 PHE cc_start: 0.7437 (p90) cc_final: 0.7150 (p90) REVERT: B 527 MET cc_start: 0.7885 (ttp) cc_final: 0.7122 (mmm) REVERT: B 638 ASP cc_start: 0.7043 (t70) cc_final: 0.6771 (t70) REVERT: B 674 MET cc_start: 0.8193 (mmt) cc_final: 0.7925 (mmp) REVERT: B 1020 PHE cc_start: 0.7936 (t80) cc_final: 0.7591 (t80) REVERT: B 1029 THR cc_start: 0.8594 (t) cc_final: 0.8134 (p) REVERT: B 1185 SER cc_start: 0.9114 (t) cc_final: 0.8718 (p) REVERT: C 542 LEU cc_start: 0.9071 (tt) cc_final: 0.8832 (tp) REVERT: C 647 TYR cc_start: 0.6464 (p90) cc_final: 0.5409 (p90) REVERT: C 752 LYS cc_start: 0.8574 (mtmm) cc_final: 0.8240 (mtpp) REVERT: C 1067 CYS cc_start: 0.5493 (p) cc_final: 0.5186 (t) REVERT: C 1116 MET cc_start: 0.7577 (tpp) cc_final: 0.7195 (tpp) REVERT: C 1136 SER cc_start: 0.8927 (t) cc_final: 0.8637 (m) REVERT: C 1179 PHE cc_start: 0.8411 (t80) cc_final: 0.8210 (t80) REVERT: C 1205 LYS cc_start: 0.6716 (mmmt) cc_final: 0.6173 (tmtt) REVERT: D 486 GLU cc_start: 0.8271 (tp30) cc_final: 0.7797 (tp30) REVERT: D 635 SER cc_start: 0.7613 (t) cc_final: 0.7195 (p) REVERT: D 719 ASP cc_start: 0.6818 (p0) cc_final: 0.6498 (p0) REVERT: D 728 ASP cc_start: 0.8029 (p0) cc_final: 0.7733 (t0) REVERT: D 1032 TRP cc_start: 0.7697 (m100) cc_final: 0.7452 (m100) REVERT: D 1116 MET cc_start: 0.7333 (mtp) cc_final: 0.6676 (mtt) REVERT: D 1126 PHE cc_start: 0.7186 (t80) cc_final: 0.6697 (t80) REVERT: D 1147 SER cc_start: 0.9140 (m) cc_final: 0.8721 (p) outliers start: 7 outliers final: 1 residues processed: 694 average time/residue: 0.3163 time to fit residues: 329.1117 Evaluate side-chains 385 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 384 time to evaluate : 2.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1044 VAL 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: A1053 ASN A1204 HIS B 747 ASN B1071 ASN B1131 HIS 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: 0.2888 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= 0.186 Angle : 0.582 9.179 26851 Z= 0.311 Chirality : 0.041 0.189 2998 Planarity : 0.005 0.061 3313 Dihedral : 9.109 110.221 2790 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.35 % Allowed : 13.81 % Favored : 83.84 % 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: -0.04 (0.16), residues: 2460 helix: 1.07 (0.13), residues: 1354 sheet: -0.54 (0.38), residues: 164 loop : -1.57 (0.18), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 766 HIS 0.020 0.002 HIS B1059 PHE 0.023 0.002 PHE A 541 TYR 0.031 0.002 TYR D1173 ARG 0.008 0.001 ARG B 453 *********************** 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 490 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 441 time to evaluate : 2.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.8841 (pp) REVERT: A 516 SER cc_start: 0.8737 (p) cc_final: 0.8415 (t) REVERT: A 619 ASN cc_start: 0.8509 (t0) cc_final: 0.8133 (t0) REVERT: A 732 TYR cc_start: 0.8963 (m-10) cc_final: 0.8625 (m-10) REVERT: A 769 ASP cc_start: 0.7156 (m-30) cc_final: 0.6929 (m-30) REVERT: A 1133 ILE cc_start: 0.8499 (mm) cc_final: 0.8258 (tp) REVERT: A 1171 ASN cc_start: 0.4700 (p0) cc_final: 0.4262 (t0) REVERT: B 408 MET cc_start: 0.7898 (mmt) cc_final: 0.7510 (mmt) REVERT: B 438 PHE cc_start: 0.7335 (p90) cc_final: 0.7026 (p90) REVERT: B 527 MET cc_start: 0.8041 (ttp) cc_final: 0.7008 (mmm) REVERT: B 1199 MET cc_start: 0.7444 (mmm) cc_final: 0.7229 (mmm) REVERT: C 432 ILE cc_start: 0.9015 (pt) cc_final: 0.8814 (tt) REVERT: C 487 GLU cc_start: 0.7507 (mt-10) cc_final: 0.7052 (mt-10) REVERT: C 620 LEU cc_start: 0.9332 (tp) cc_final: 0.9048 (tp) REVERT: C 647 TYR cc_start: 0.6644 (p90) cc_final: 0.4964 (p90) REVERT: C 670 MET cc_start: 0.7298 (mmt) cc_final: 0.6001 (mmm) REVERT: C 761 LYS cc_start: 0.8144 (ttpm) cc_final: 0.7829 (pttp) REVERT: C 1080 ASP cc_start: 0.6992 (t70) cc_final: 0.6506 (p0) REVERT: C 1116 MET cc_start: 0.7546 (tpp) cc_final: 0.7156 (tpp) REVERT: C 1136 SER cc_start: 0.8793 (t) cc_final: 0.8577 (t) REVERT: C 1205 LYS cc_start: 0.6948 (mmmt) cc_final: 0.6374 (tptp) REVERT: D 604 VAL cc_start: 0.9098 (t) cc_final: 0.8664 (m) REVERT: D 635 SER cc_start: 0.7829 (t) cc_final: 0.7561 (p) REVERT: D 651 ASP cc_start: 0.7848 (t0) cc_final: 0.7557 (t0) REVERT: D 728 ASP cc_start: 0.8155 (p0) cc_final: 0.7835 (t0) REVERT: D 783 LYS cc_start: 0.6480 (tptt) cc_final: 0.5763 (tptp) REVERT: D 1096 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7704 (t80) REVERT: D 1147 SER cc_start: 0.8958 (m) cc_final: 0.8651 (p) outliers start: 49 outliers final: 26 residues processed: 470 average time/residue: 0.2826 time to fit residues: 210.5047 Evaluate side-chains 372 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 344 time to evaluate : 2.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 791 ASN Chi-restraints excluded: chain B residue 1120 CYS Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain C residue 425 CYS Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 1027 VAL Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 714 GLN Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 1055 GLU Chi-restraints excluded: chain D residue 1096 PHE Chi-restraints excluded: chain D residue 1187 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 124 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 186 optimal weight: 0.1980 chunk 152 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 224 optimal weight: 6.9990 chunk 242 optimal weight: 6.9990 chunk 200 optimal weight: 3.9990 chunk 222 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 180 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1204 HIS ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 714 GLN C1053 ASN D1008 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 19872 Z= 0.226 Angle : 0.569 10.122 26851 Z= 0.301 Chirality : 0.041 0.212 2998 Planarity : 0.004 0.036 3313 Dihedral : 8.799 106.622 2790 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.36 % Allowed : 15.06 % Favored : 81.58 % 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: 0.47 (0.16), residues: 2460 helix: 1.63 (0.14), residues: 1357 sheet: -0.51 (0.38), residues: 159 loop : -1.54 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 460 HIS 0.019 0.002 HIS B1059 PHE 0.017 0.002 PHE A 541 TYR 0.024 0.002 TYR B1173 ARG 0.005 0.000 ARG C1064 *********************** 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 443 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 373 time to evaluate : 2.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.8933 (pp) REVERT: A 516 SER cc_start: 0.8776 (p) cc_final: 0.8477 (t) REVERT: A 619 ASN cc_start: 0.8539 (t0) cc_final: 0.8255 (t0) REVERT: A 1063 TRP cc_start: 0.6206 (m-10) cc_final: 0.5797 (m100) REVERT: B 438 PHE cc_start: 0.7348 (p90) cc_final: 0.7000 (p90) REVERT: B 709 ASN cc_start: 0.9003 (t0) cc_final: 0.8760 (t0) REVERT: B 1020 PHE cc_start: 0.7988 (t80) cc_final: 0.7708 (t80) REVERT: B 1185 SER cc_start: 0.9122 (t) cc_final: 0.8919 (p) REVERT: B 1199 MET cc_start: 0.7543 (mmm) cc_final: 0.7252 (mmm) REVERT: C 503 MET cc_start: 0.8405 (ttp) cc_final: 0.8144 (ttp) REVERT: C 620 LEU cc_start: 0.9383 (tp) cc_final: 0.9143 (tp) REVERT: C 647 TYR cc_start: 0.6556 (p90) cc_final: 0.5520 (p90) REVERT: C 1078 GLN cc_start: 0.6839 (pp30) cc_final: 0.6050 (mt0) REVERT: C 1103 SER cc_start: 0.7513 (m) cc_final: 0.7225 (p) REVERT: C 1116 MET cc_start: 0.7560 (tpp) cc_final: 0.7266 (tpp) REVERT: C 1130 ARG cc_start: 0.7120 (mmp80) cc_final: 0.6836 (mmp80) REVERT: C 1136 SER cc_start: 0.8771 (t) cc_final: 0.8556 (t) REVERT: C 1205 LYS cc_start: 0.7024 (mmmt) cc_final: 0.6530 (tmtt) REVERT: D 635 SER cc_start: 0.7926 (t) cc_final: 0.7635 (p) REVERT: D 728 ASP cc_start: 0.8190 (p0) cc_final: 0.7871 (t0) REVERT: D 783 LYS cc_start: 0.6494 (tptt) cc_final: 0.5855 (tptp) REVERT: D 1147 SER cc_start: 0.8986 (m) cc_final: 0.8687 (p) outliers start: 70 outliers final: 55 residues processed: 414 average time/residue: 0.2571 time to fit residues: 171.8426 Evaluate side-chains 391 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 335 time to evaluate : 2.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1030 ASP Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 791 ASN Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1120 CYS Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 425 CYS Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain C residue 1027 VAL Chi-restraints excluded: chain C residue 1038 VAL Chi-restraints excluded: chain C residue 1066 CYS Chi-restraints excluded: chain C residue 1129 THR Chi-restraints excluded: chain C residue 1149 ILE Chi-restraints excluded: chain C residue 1154 VAL Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 674 MET Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 764 ASN Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1111 VAL Chi-restraints excluded: chain D residue 1154 VAL Chi-restraints excluded: chain D residue 1184 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 222 optimal weight: 0.0060 chunk 168 optimal weight: 7.9990 chunk 116 optimal weight: 0.8980 chunk 24 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 150 optimal weight: 2.9990 chunk 225 optimal weight: 7.9990 chunk 238 optimal weight: 0.5980 chunk 117 optimal weight: 2.9990 chunk 213 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 overall best weight: 1.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 ASN A1159 ASN ** B 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1204 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3619 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= 0.221 Angle : 0.553 8.908 26851 Z= 0.292 Chirality : 0.041 0.227 2998 Planarity : 0.004 0.046 3313 Dihedral : 8.563 104.450 2790 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.56 % Allowed : 15.64 % Favored : 79.81 % 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: 0.61 (0.17), residues: 2460 helix: 1.78 (0.14), residues: 1358 sheet: -0.77 (0.37), residues: 171 loop : -1.49 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 460 HIS 0.010 0.001 HIS D1059 PHE 0.018 0.001 PHE A 541 TYR 0.024 0.001 TYR A 768 ARG 0.003 0.000 ARG B 453 *********************** 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 448 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 353 time to evaluate : 2.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.8178 (ttp) REVERT: A 498 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.9015 (pp) REVERT: A 516 SER cc_start: 0.8811 (p) cc_final: 0.8508 (t) REVERT: A 619 ASN cc_start: 0.8569 (t0) cc_final: 0.8279 (t0) REVERT: A 1063 TRP cc_start: 0.6243 (m-10) cc_final: 0.5841 (m100) REVERT: B 438 PHE cc_start: 0.7348 (p90) cc_final: 0.7025 (p90) REVERT: B 670 MET cc_start: 0.8380 (mmt) cc_final: 0.8161 (mtt) REVERT: B 709 ASN cc_start: 0.8939 (t0) cc_final: 0.8550 (t0) REVERT: B 746 VAL cc_start: 0.9177 (t) cc_final: 0.8836 (p) REVERT: B 1020 PHE cc_start: 0.7977 (t80) cc_final: 0.7700 (t80) REVERT: B 1185 SER cc_start: 0.9124 (t) cc_final: 0.8919 (p) REVERT: B 1199 MET cc_start: 0.7592 (mmm) cc_final: 0.7295 (mmm) REVERT: C 620 LEU cc_start: 0.9397 (tp) cc_final: 0.9165 (tp) REVERT: C 647 TYR cc_start: 0.6637 (p90) cc_final: 0.5488 (p90) REVERT: C 1040 LYS cc_start: 0.3014 (OUTLIER) cc_final: 0.2445 (mttt) REVERT: C 1078 GLN cc_start: 0.6812 (pp30) cc_final: 0.6134 (mt0) REVERT: C 1103 SER cc_start: 0.7688 (m) cc_final: 0.7439 (p) REVERT: C 1116 MET cc_start: 0.7553 (tpp) cc_final: 0.7279 (tpp) REVERT: C 1136 SER cc_start: 0.8741 (t) cc_final: 0.8525 (t) REVERT: C 1205 LYS cc_start: 0.7123 (mmmt) cc_final: 0.6578 (tmtt) REVERT: D 635 SER cc_start: 0.7967 (t) cc_final: 0.7646 (p) REVERT: D 728 ASP cc_start: 0.8182 (p0) cc_final: 0.7830 (t0) REVERT: D 1147 SER cc_start: 0.9012 (m) cc_final: 0.8698 (p) outliers start: 95 outliers final: 70 residues processed: 415 average time/residue: 0.2711 time to fit residues: 181.3775 Evaluate side-chains 401 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 328 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1030 ASP Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 546 PHE Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 791 ASN Chi-restraints excluded: chain B residue 1030 ASP Chi-restraints excluded: chain B residue 1082 PHE Chi-restraints excluded: chain B residue 1120 CYS Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 425 CYS Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 435 HIS Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain C residue 1027 VAL Chi-restraints excluded: chain C residue 1039 CYS Chi-restraints excluded: chain C residue 1040 LYS Chi-restraints excluded: chain C residue 1076 CYS Chi-restraints excluded: chain C residue 1109 LEU Chi-restraints excluded: chain C residue 1129 THR Chi-restraints excluded: chain C residue 1149 ILE Chi-restraints excluded: chain C residue 1154 VAL Chi-restraints excluded: chain C residue 1194 VAL Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 674 MET Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 764 ASN Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1111 VAL Chi-restraints excluded: chain D residue 1143 SER Chi-restraints excluded: chain D residue 1154 VAL Chi-restraints excluded: chain D residue 1184 LEU Chi-restraints excluded: chain D residue 1187 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 198 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 177 optimal weight: 7.9990 chunk 98 optimal weight: 0.0970 chunk 203 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 121 optimal weight: 4.9990 chunk 214 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1053 ASN ** B 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1008 GLN B1204 HIS C1204 HIS D 586 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19872 Z= 0.227 Angle : 0.554 11.593 26851 Z= 0.290 Chirality : 0.041 0.243 2998 Planarity : 0.004 0.043 3313 Dihedral : 8.403 102.303 2790 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.70 % Allowed : 16.31 % 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: 0.64 (0.17), residues: 2460 helix: 1.83 (0.14), residues: 1359 sheet: -0.92 (0.38), residues: 168 loop : -1.49 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 460 HIS 0.019 0.002 HIS B1059 PHE 0.021 0.001 PHE A 541 TYR 0.027 0.002 TYR A 732 ARG 0.004 0.000 ARG D1064 *********************** 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 447 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 349 time to evaluate : 2.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8193 (ttp) REVERT: A 498 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8767 (pp) REVERT: A 516 SER cc_start: 0.8820 (p) cc_final: 0.8504 (t) REVERT: A 619 ASN cc_start: 0.8601 (t0) cc_final: 0.8327 (t0) REVERT: A 1063 TRP cc_start: 0.6342 (m-10) cc_final: 0.5913 (m100) REVERT: B 438 PHE cc_start: 0.7403 (p90) cc_final: 0.7157 (p90) REVERT: B 521 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8758 (mt) REVERT: B 709 ASN cc_start: 0.9042 (t0) cc_final: 0.8741 (t0) REVERT: B 746 VAL cc_start: 0.9208 (t) cc_final: 0.8913 (p) REVERT: B 1017 PHE cc_start: 0.7704 (t80) cc_final: 0.7423 (t80) REVERT: B 1020 PHE cc_start: 0.8042 (t80) cc_final: 0.7777 (t80) REVERT: B 1185 SER cc_start: 0.9125 (t) cc_final: 0.8919 (p) REVERT: B 1199 MET cc_start: 0.7622 (mmm) cc_final: 0.7306 (mmp) REVERT: C 647 TYR cc_start: 0.6382 (p90) cc_final: 0.5546 (p90) REVERT: C 670 MET cc_start: 0.7292 (mmt) cc_final: 0.6658 (mmm) REVERT: C 705 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7993 (mm-30) REVERT: C 1009 MET cc_start: 0.8778 (mmm) cc_final: 0.8448 (mmm) REVERT: C 1040 LYS cc_start: 0.3402 (OUTLIER) cc_final: 0.2783 (mttt) REVERT: C 1078 GLN cc_start: 0.6807 (pp30) cc_final: 0.6181 (mt0) REVERT: C 1103 SER cc_start: 0.7741 (m) cc_final: 0.7531 (p) REVERT: C 1116 MET cc_start: 0.7601 (tpp) cc_final: 0.7309 (tpp) REVERT: C 1136 SER cc_start: 0.8736 (t) cc_final: 0.8526 (t) REVERT: C 1205 LYS cc_start: 0.7054 (mmmt) cc_final: 0.6607 (tmtt) REVERT: D 635 SER cc_start: 0.8056 (t) cc_final: 0.7690 (p) REVERT: D 728 ASP cc_start: 0.8154 (p0) cc_final: 0.7796 (t0) REVERT: D 783 LYS cc_start: 0.6869 (tptt) cc_final: 0.6572 (tptp) REVERT: D 1147 SER cc_start: 0.9025 (m) cc_final: 0.8714 (p) outliers start: 98 outliers final: 71 residues processed: 411 average time/residue: 0.2724 time to fit residues: 180.7923 Evaluate side-chains 403 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 327 time to evaluate : 2.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1030 ASP Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 546 PHE Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 791 ASN Chi-restraints excluded: chain B residue 1030 ASP Chi-restraints excluded: chain B residue 1082 PHE Chi-restraints excluded: chain B residue 1120 CYS Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 425 CYS Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 435 HIS Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 1027 VAL Chi-restraints excluded: chain C residue 1038 VAL Chi-restraints excluded: chain C residue 1039 CYS Chi-restraints excluded: chain C residue 1040 LYS Chi-restraints excluded: chain C residue 1065 THR Chi-restraints excluded: chain C residue 1076 CYS Chi-restraints excluded: chain C residue 1109 LEU Chi-restraints excluded: chain C residue 1129 THR Chi-restraints excluded: chain C residue 1149 ILE Chi-restraints excluded: chain C residue 1154 VAL Chi-restraints excluded: chain C residue 1194 VAL Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 674 MET Chi-restraints excluded: chain D residue 719 ASP Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 764 ASN Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1111 VAL Chi-restraints excluded: chain D residue 1154 VAL Chi-restraints excluded: chain D residue 1184 LEU Chi-restraints excluded: chain D residue 1187 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 80 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 238 optimal weight: 0.0870 chunk 198 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 79 optimal weight: 0.0570 chunk 125 optimal weight: 7.9990 overall best weight: 1.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 ASN ** B 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1204 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19872 Z= 0.233 Angle : 0.558 12.127 26851 Z= 0.290 Chirality : 0.041 0.254 2998 Planarity : 0.004 0.040 3313 Dihedral : 8.290 99.506 2790 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.80 % Allowed : 17.07 % 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: 0.63 (0.17), residues: 2460 helix: 1.83 (0.14), residues: 1358 sheet: -0.84 (0.37), residues: 174 loop : -1.54 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 460 HIS 0.029 0.002 HIS B1204 PHE 0.016 0.001 PHE A 541 TYR 0.028 0.001 TYR A 732 ARG 0.007 0.000 ARG D 594 *********************** 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 446 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 346 time to evaluate : 2.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.8224 (ttp) REVERT: A 508 GLN cc_start: 0.7773 (pp30) cc_final: 0.7471 (pp30) REVERT: A 619 ASN cc_start: 0.8618 (t0) cc_final: 0.8352 (t0) REVERT: A 633 ILE cc_start: 0.9062 (tp) cc_final: 0.8710 (mt) REVERT: A 1063 TRP cc_start: 0.6377 (m-10) cc_final: 0.5942 (m100) REVERT: A 1171 ASN cc_start: 0.5144 (p0) cc_final: 0.4653 (m-40) REVERT: B 521 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8770 (mt) REVERT: B 709 ASN cc_start: 0.9055 (t0) cc_final: 0.8782 (t0) REVERT: B 746 VAL cc_start: 0.9231 (t) cc_final: 0.8964 (p) REVERT: B 1017 PHE cc_start: 0.7725 (t80) cc_final: 0.7444 (t80) REVERT: B 1020 PHE cc_start: 0.8037 (t80) cc_final: 0.7787 (t80) REVERT: B 1185 SER cc_start: 0.9128 (t) cc_final: 0.8923 (p) REVERT: B 1199 MET cc_start: 0.7627 (mmm) cc_final: 0.7305 (mmp) REVERT: C 647 TYR cc_start: 0.6475 (p90) cc_final: 0.4791 (p90) REVERT: C 670 MET cc_start: 0.7343 (mmt) cc_final: 0.5992 (mmm) REVERT: C 705 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7985 (mm-30) REVERT: C 1040 LYS cc_start: 0.3444 (OUTLIER) cc_final: 0.2796 (mttt) REVERT: C 1078 GLN cc_start: 0.6855 (pp30) cc_final: 0.6304 (mt0) REVERT: C 1116 MET cc_start: 0.7613 (tpp) cc_final: 0.7379 (tpp) REVERT: C 1205 LYS cc_start: 0.7047 (mmmt) cc_final: 0.6595 (tmtt) REVERT: D 635 SER cc_start: 0.8013 (t) cc_final: 0.7646 (p) REVERT: D 647 TYR cc_start: 0.6870 (OUTLIER) cc_final: 0.6320 (m-80) REVERT: D 728 ASP cc_start: 0.8205 (p0) cc_final: 0.7750 (t0) REVERT: D 1147 SER cc_start: 0.9018 (m) cc_final: 0.8736 (p) outliers start: 100 outliers final: 76 residues processed: 406 average time/residue: 0.2729 time to fit residues: 177.6061 Evaluate side-chains 409 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 328 time to evaluate : 2.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 768 TYR Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1030 ASP Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 791 ASN Chi-restraints excluded: chain B residue 1030 ASP Chi-restraints excluded: chain B residue 1082 PHE Chi-restraints excluded: chain B residue 1120 CYS Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 435 HIS Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 1027 VAL Chi-restraints excluded: chain C residue 1038 VAL Chi-restraints excluded: chain C residue 1039 CYS Chi-restraints excluded: chain C residue 1040 LYS Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1065 THR Chi-restraints excluded: chain C residue 1076 CYS Chi-restraints excluded: chain C residue 1109 LEU Chi-restraints excluded: chain C residue 1129 THR Chi-restraints excluded: chain C residue 1149 ILE Chi-restraints excluded: chain C residue 1154 VAL Chi-restraints excluded: chain C residue 1194 VAL Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 674 MET Chi-restraints excluded: chain D residue 718 CYS Chi-restraints excluded: chain D residue 719 ASP Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 764 ASN Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1055 GLU Chi-restraints excluded: chain D residue 1096 PHE Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1143 SER Chi-restraints excluded: chain D residue 1154 VAL Chi-restraints excluded: chain D residue 1184 LEU Chi-restraints excluded: chain D residue 1187 ILE 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: 7.9990 chunk 136 optimal weight: 1.9990 chunk 174 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 201 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 238 optimal weight: 0.9990 chunk 148 optimal weight: 8.9990 chunk 145 optimal weight: 0.0050 chunk 109 optimal weight: 8.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 587 GLN ** B 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1204 HIS C 709 ASN C1204 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19872 Z= 0.179 Angle : 0.532 9.952 26851 Z= 0.276 Chirality : 0.040 0.253 2998 Planarity : 0.003 0.040 3313 Dihedral : 8.048 97.303 2790 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.22 % Allowed : 17.94 % Favored : 77.84 % 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: 1.92 (0.14), residues: 1359 sheet: -0.96 (0.37), residues: 173 loop : -1.53 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 460 HIS 0.008 0.001 HIS D1059 PHE 0.013 0.001 PHE A 541 TYR 0.018 0.001 TYR D1173 ARG 0.008 0.000 ARG D 594 *********************** 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 437 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 349 time to evaluate : 2.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 LYS cc_start: 0.7196 (OUTLIER) cc_final: 0.6723 (pmmt) REVERT: A 619 ASN cc_start: 0.8552 (t0) cc_final: 0.8264 (t0) REVERT: A 633 ILE cc_start: 0.9062 (tp) cc_final: 0.8732 (mt) REVERT: A 714 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.7192 (mm110) REVERT: A 1063 TRP cc_start: 0.6386 (m-10) cc_final: 0.5927 (m100) REVERT: A 1171 ASN cc_start: 0.5137 (p0) cc_final: 0.4683 (m-40) REVERT: B 521 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8753 (mt) REVERT: B 709 ASN cc_start: 0.9071 (t0) cc_final: 0.8815 (t0) REVERT: B 746 VAL cc_start: 0.9235 (t) cc_final: 0.8996 (p) REVERT: B 1017 PHE cc_start: 0.7705 (t80) cc_final: 0.7436 (t80) REVERT: B 1020 PHE cc_start: 0.8021 (t80) cc_final: 0.7787 (t80) REVERT: B 1185 SER cc_start: 0.9141 (t) cc_final: 0.8930 (p) REVERT: B 1199 MET cc_start: 0.7597 (mmm) cc_final: 0.7293 (mmp) REVERT: C 647 TYR cc_start: 0.6512 (p90) cc_final: 0.4879 (p90) REVERT: C 670 MET cc_start: 0.7345 (mmt) cc_final: 0.5995 (mmm) REVERT: C 705 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8018 (mm-30) REVERT: C 1039 CYS cc_start: 0.3704 (OUTLIER) cc_final: 0.3466 (p) REVERT: C 1040 LYS cc_start: 0.3648 (OUTLIER) cc_final: 0.3060 (mttt) REVERT: C 1078 GLN cc_start: 0.6942 (pp30) cc_final: 0.6346 (mt0) REVERT: C 1116 MET cc_start: 0.7605 (tpp) cc_final: 0.7370 (tpp) REVERT: C 1205 LYS cc_start: 0.7095 (mmmt) cc_final: 0.6643 (tmtt) REVERT: D 635 SER cc_start: 0.8028 (t) cc_final: 0.7665 (p) REVERT: D 728 ASP cc_start: 0.8229 (p0) cc_final: 0.7756 (t0) REVERT: D 1147 SER cc_start: 0.9016 (m) cc_final: 0.8734 (p) outliers start: 88 outliers final: 65 residues processed: 408 average time/residue: 0.2696 time to fit residues: 176.6671 Evaluate side-chains 399 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 328 time to evaluate : 2.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 714 GLN Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 768 TYR Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 587 GLN Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 791 ASN Chi-restraints excluded: chain B residue 1030 ASP Chi-restraints excluded: chain B residue 1059 HIS Chi-restraints excluded: chain B residue 1120 CYS Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 425 CYS Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 435 HIS Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 1039 CYS Chi-restraints excluded: chain C residue 1040 LYS Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1065 THR Chi-restraints excluded: chain C residue 1076 CYS Chi-restraints excluded: chain C residue 1129 THR Chi-restraints excluded: chain C residue 1154 VAL Chi-restraints excluded: chain C residue 1194 VAL Chi-restraints excluded: chain C residue 1204 HIS Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 718 CYS Chi-restraints excluded: chain D residue 719 ASP Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 764 ASN Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1055 GLU Chi-restraints excluded: chain D residue 1143 SER Chi-restraints excluded: chain D residue 1154 VAL Chi-restraints excluded: chain D residue 1184 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 147 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 46 optimal weight: 0.2980 chunk 151 optimal weight: 0.8980 chunk 162 optimal weight: 0.4980 chunk 117 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 187 optimal weight: 5.9990 chunk 216 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1204 HIS C1204 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4241 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= 0.165 Angle : 0.542 9.478 26851 Z= 0.277 Chirality : 0.040 0.247 2998 Planarity : 0.003 0.040 3313 Dihedral : 7.860 95.515 2790 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.69 % Allowed : 18.71 % Favored : 77.60 % 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: 0.75 (0.17), residues: 2460 helix: 1.97 (0.14), residues: 1360 sheet: -0.95 (0.38), residues: 164 loop : -1.53 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 460 HIS 0.015 0.002 HIS B1204 PHE 0.012 0.001 PHE A 541 TYR 0.019 0.001 TYR D1173 ARG 0.008 0.000 ARG D 594 *********************** 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 426 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 349 time to evaluate : 2.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 LYS cc_start: 0.7198 (OUTLIER) cc_final: 0.6711 (pmmt) REVERT: A 619 ASN cc_start: 0.8573 (t0) cc_final: 0.8309 (t0) REVERT: A 633 ILE cc_start: 0.9046 (tp) cc_final: 0.8709 (mt) REVERT: A 714 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.7148 (mm110) REVERT: A 1063 TRP cc_start: 0.6385 (m-10) cc_final: 0.5912 (m100) REVERT: A 1171 ASN cc_start: 0.5132 (p0) cc_final: 0.4698 (m-40) REVERT: B 709 ASN cc_start: 0.9039 (t0) cc_final: 0.8793 (t0) REVERT: B 746 VAL cc_start: 0.9248 (t) cc_final: 0.9026 (p) REVERT: B 1017 PHE cc_start: 0.7727 (t80) cc_final: 0.7479 (t80) REVERT: B 1020 PHE cc_start: 0.8006 (t80) cc_final: 0.7769 (t80) REVERT: B 1185 SER cc_start: 0.9141 (t) cc_final: 0.8934 (p) REVERT: B 1199 MET cc_start: 0.7602 (mmm) cc_final: 0.7279 (mmp) REVERT: C 511 LYS cc_start: 0.7589 (mptp) cc_final: 0.7361 (tttm) REVERT: C 596 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8632 (mm) REVERT: C 647 TYR cc_start: 0.6471 (p90) cc_final: 0.5626 (p90) REVERT: C 670 MET cc_start: 0.7394 (mmt) cc_final: 0.6786 (mmm) REVERT: C 705 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8078 (mm-30) REVERT: C 1078 GLN cc_start: 0.7009 (pp30) cc_final: 0.6421 (mt0) REVERT: C 1116 MET cc_start: 0.7591 (tpp) cc_final: 0.7381 (tpp) REVERT: C 1205 LYS cc_start: 0.6951 (mmmt) cc_final: 0.6581 (tmtt) REVERT: D 635 SER cc_start: 0.8007 (t) cc_final: 0.7645 (p) REVERT: D 670 MET cc_start: 0.8913 (ttm) cc_final: 0.8315 (ttm) REVERT: D 728 ASP cc_start: 0.8209 (p0) cc_final: 0.7732 (t0) REVERT: D 1096 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7675 (t80) REVERT: D 1147 SER cc_start: 0.9011 (m) cc_final: 0.8753 (p) outliers start: 77 outliers final: 60 residues processed: 395 average time/residue: 0.2722 time to fit residues: 171.4686 Evaluate side-chains 401 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 336 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 714 GLN Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 768 TYR Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 791 ASN Chi-restraints excluded: chain B residue 1059 HIS Chi-restraints excluded: chain B residue 1120 CYS Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 435 HIS Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 1040 LYS Chi-restraints excluded: chain C residue 1065 THR Chi-restraints excluded: chain C residue 1076 CYS Chi-restraints excluded: chain C residue 1129 THR Chi-restraints excluded: chain C residue 1154 VAL Chi-restraints excluded: chain C residue 1194 VAL Chi-restraints excluded: chain C residue 1204 HIS Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 718 CYS Chi-restraints excluded: chain D residue 719 ASP Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 764 ASN Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1055 GLU Chi-restraints excluded: chain D residue 1096 PHE Chi-restraints excluded: chain D residue 1143 SER Chi-restraints excluded: chain D residue 1154 VAL Chi-restraints excluded: chain D residue 1184 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 228 optimal weight: 4.9990 chunk 208 optimal weight: 1.9990 chunk 221 optimal weight: 0.0470 chunk 133 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 200 optimal weight: 4.9990 chunk 209 optimal weight: 8.9990 chunk 145 optimal weight: 0.0980 chunk 234 optimal weight: 3.9990 overall best weight: 1.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 587 GLN ** B 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1204 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19872 Z= 0.197 Angle : 0.558 9.137 26851 Z= 0.285 Chirality : 0.040 0.249 2998 Planarity : 0.004 0.084 3313 Dihedral : 7.821 95.335 2790 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.50 % Allowed : 19.33 % Favored : 77.17 % 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: 0.70 (0.17), residues: 2460 helix: 1.93 (0.14), residues: 1358 sheet: -0.86 (0.38), residues: 167 loop : -1.56 (0.19), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 460 HIS 0.008 0.001 HIS C1081 PHE 0.016 0.001 PHE C1082 TYR 0.018 0.001 TYR D1173 ARG 0.017 0.000 ARG C1203 *********************** 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 410 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 337 time to evaluate : 2.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 LYS cc_start: 0.7086 (OUTLIER) cc_final: 0.6620 (pmmt) REVERT: A 619 ASN cc_start: 0.8597 (t0) cc_final: 0.8332 (t0) REVERT: A 633 ILE cc_start: 0.9050 (tp) cc_final: 0.8698 (mt) REVERT: A 714 GLN cc_start: 0.7500 (OUTLIER) cc_final: 0.7162 (mm110) REVERT: A 1063 TRP cc_start: 0.6410 (m-10) cc_final: 0.5958 (m100) REVERT: A 1171 ASN cc_start: 0.5147 (p0) cc_final: 0.4698 (m-40) REVERT: B 709 ASN cc_start: 0.9058 (t0) cc_final: 0.8802 (t0) REVERT: B 746 VAL cc_start: 0.9247 (t) cc_final: 0.9028 (p) REVERT: B 1017 PHE cc_start: 0.7740 (t80) cc_final: 0.7495 (t80) REVERT: B 1020 PHE cc_start: 0.8042 (t80) cc_final: 0.7802 (t80) REVERT: B 1185 SER cc_start: 0.9144 (t) cc_final: 0.8920 (p) REVERT: B 1199 MET cc_start: 0.7585 (mmm) cc_final: 0.7255 (mmp) REVERT: C 511 LYS cc_start: 0.7576 (mptp) cc_final: 0.7358 (tttm) REVERT: C 647 TYR cc_start: 0.6476 (p90) cc_final: 0.5663 (p90) REVERT: C 670 MET cc_start: 0.7450 (mmt) cc_final: 0.6893 (mmt) REVERT: C 705 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8110 (mm-30) REVERT: C 819 ARG cc_start: 0.5853 (mmp80) cc_final: 0.5262 (mtm-85) REVERT: C 1040 LYS cc_start: 0.3906 (OUTLIER) cc_final: 0.3344 (mttt) REVERT: C 1078 GLN cc_start: 0.7011 (pp30) cc_final: 0.6438 (mt0) REVERT: C 1116 MET cc_start: 0.7593 (tpp) cc_final: 0.7380 (tpp) REVERT: C 1205 LYS cc_start: 0.6872 (mmmt) cc_final: 0.6552 (tmtt) REVERT: D 635 SER cc_start: 0.8005 (t) cc_final: 0.7644 (p) REVERT: D 670 MET cc_start: 0.9011 (ttm) cc_final: 0.8671 (ttm) REVERT: D 728 ASP cc_start: 0.8199 (p0) cc_final: 0.7720 (t0) REVERT: D 1147 SER cc_start: 0.8941 (m) cc_final: 0.8704 (p) outliers start: 73 outliers final: 61 residues processed: 383 average time/residue: 0.2756 time to fit residues: 168.6224 Evaluate side-chains 394 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 329 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 714 GLN Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 768 TYR Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 791 ASN Chi-restraints excluded: chain B residue 1059 HIS Chi-restraints excluded: chain B residue 1120 CYS Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 425 CYS Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 435 HIS Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 1038 VAL Chi-restraints excluded: chain C residue 1040 LYS Chi-restraints excluded: chain C residue 1065 THR Chi-restraints excluded: chain C residue 1076 CYS Chi-restraints excluded: chain C residue 1129 THR Chi-restraints excluded: chain C residue 1154 VAL Chi-restraints excluded: chain C residue 1194 VAL Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 718 CYS Chi-restraints excluded: chain D residue 719 ASP Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 764 ASN Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1055 GLU Chi-restraints excluded: chain D residue 1096 PHE Chi-restraints excluded: chain D residue 1143 SER Chi-restraints excluded: chain D residue 1154 VAL Chi-restraints excluded: chain D residue 1184 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 143 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 163 optimal weight: 0.7980 chunk 246 optimal weight: 4.9990 chunk 226 optimal weight: 6.9990 chunk 195 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 151 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 208 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1204 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19872 Z= 0.168 Angle : 0.559 9.197 26851 Z= 0.284 Chirality : 0.040 0.245 2998 Planarity : 0.003 0.060 3313 Dihedral : 7.624 93.301 2790 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.88 % Allowed : 20.14 % Favored : 76.98 % 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: 1.98 (0.14), residues: 1359 sheet: -0.86 (0.38), residues: 170 loop : -1.57 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D1063 HIS 0.008 0.001 HIS D1059 PHE 0.017 0.001 PHE C1082 TYR 0.017 0.001 TYR D1173 ARG 0.012 0.000 ARG C1203 ********************** 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 402 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 342 time to evaluate : 2.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 619 ASN cc_start: 0.8587 (t0) cc_final: 0.8313 (t0) REVERT: A 633 ILE cc_start: 0.9067 (tp) cc_final: 0.8712 (mt) REVERT: A 1063 TRP cc_start: 0.6392 (m-10) cc_final: 0.5961 (m100) REVERT: A 1171 ASN cc_start: 0.5144 (p0) cc_final: 0.4708 (m-40) REVERT: B 463 MET cc_start: 0.8021 (tpp) cc_final: 0.7772 (mtp) REVERT: B 709 ASN cc_start: 0.9043 (t0) cc_final: 0.8617 (t0) REVERT: B 746 VAL cc_start: 0.9239 (t) cc_final: 0.9025 (p) REVERT: B 1017 PHE cc_start: 0.7752 (t80) cc_final: 0.7525 (t80) REVERT: B 1020 PHE cc_start: 0.8023 (t80) cc_final: 0.7809 (t80) REVERT: B 1098 ARG cc_start: 0.8116 (mmm160) cc_final: 0.7454 (mmp80) REVERT: B 1104 SER cc_start: 0.9052 (m) cc_final: 0.8709 (t) REVERT: B 1185 SER cc_start: 0.9142 (t) cc_final: 0.8909 (p) REVERT: B 1199 MET cc_start: 0.7573 (mmm) cc_final: 0.7237 (mmp) REVERT: C 402 GLU cc_start: 0.7466 (tp30) cc_final: 0.7149 (tp30) REVERT: C 511 LYS cc_start: 0.7561 (mptp) cc_final: 0.7334 (tttm) REVERT: C 647 TYR cc_start: 0.6482 (p90) cc_final: 0.5324 (p90) REVERT: C 670 MET cc_start: 0.7481 (mmt) cc_final: 0.6313 (mmm) REVERT: C 705 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8122 (mm-30) REVERT: C 819 ARG cc_start: 0.5778 (mmp80) cc_final: 0.5240 (mtm-85) REVERT: C 1040 LYS cc_start: 0.3885 (OUTLIER) cc_final: 0.3563 (mttm) REVERT: C 1078 GLN cc_start: 0.7043 (pp30) cc_final: 0.6482 (mt0) REVERT: C 1116 MET cc_start: 0.7597 (tpp) cc_final: 0.7388 (tpp) REVERT: C 1205 LYS cc_start: 0.7001 (mmmt) cc_final: 0.6617 (tmtt) REVERT: D 416 GLU cc_start: 0.7293 (mm-30) cc_final: 0.7061 (pp20) REVERT: D 476 ILE cc_start: 0.8769 (mt) cc_final: 0.8542 (mm) REVERT: D 635 SER cc_start: 0.8000 (t) cc_final: 0.7651 (p) REVERT: D 728 ASP cc_start: 0.8194 (p0) cc_final: 0.7721 (t0) REVERT: D 1096 PHE cc_start: 0.8092 (OUTLIER) cc_final: 0.7671 (t80) REVERT: D 1147 SER cc_start: 0.8929 (m) cc_final: 0.8717 (p) outliers start: 60 outliers final: 49 residues processed: 379 average time/residue: 0.2757 time to fit residues: 165.9646 Evaluate side-chains 388 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 336 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 791 ASN Chi-restraints excluded: chain B residue 1120 CYS Chi-restraints excluded: chain B residue 1153 ILE Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 435 HIS Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 1040 LYS Chi-restraints excluded: chain C residue 1065 THR Chi-restraints excluded: chain C residue 1076 CYS Chi-restraints excluded: chain C residue 1129 THR Chi-restraints excluded: chain C residue 1154 VAL Chi-restraints excluded: chain C residue 1194 VAL Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 719 ASP Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 764 ASN Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1063 TRP Chi-restraints excluded: chain D residue 1096 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 60 optimal weight: 0.7980 chunk 180 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 54 optimal weight: 0.0980 chunk 196 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 201 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 172 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.125984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.099233 restraints weight = 38390.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.101727 restraints weight = 23358.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.103345 restraints weight = 17306.928| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19872 Z= 0.211 Angle : 0.575 9.413 26851 Z= 0.293 Chirality : 0.041 0.245 2998 Planarity : 0.004 0.057 3313 Dihedral : 7.633 93.749 2790 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.07 % Allowed : 19.95 % Favored : 76.98 % 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: 0.68 (0.17), residues: 2460 helix: 1.92 (0.14), residues: 1359 sheet: -0.77 (0.38), residues: 174 loop : -1.61 (0.19), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 460 HIS 0.012 0.002 HIS B1204 PHE 0.017 0.001 PHE C1082 TYR 0.020 0.001 TYR B 797 ARG 0.011 0.000 ARG C1203 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4404.40 seconds wall clock time: 81 minutes 34.75 seconds (4894.75 seconds total)