Starting phenix.real_space_refine on Sat Mar 16 05:57:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6upk_20840/03_2024/6upk_20840.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6upk_20840/03_2024/6upk_20840.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6upk_20840/03_2024/6upk_20840.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6upk_20840/03_2024/6upk_20840.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6upk_20840/03_2024/6upk_20840.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6upk_20840/03_2024/6upk_20840.pdb" } resolution = 4.9 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= 0.005 sd= 0.025 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 P 144 5.49 5 S 44 5.16 5 C 8349 2.51 5 N 2497 2.21 5 O 2827 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 31": "NH1" <-> "NH2" Residue "G ARG 525": "NH1" <-> "NH2" Residue "G ARG 581": "NH1" <-> "NH2" Residue "G ARG 623": "NH1" <-> "NH2" Residue "G ARG 631": "NH1" <-> "NH2" Residue "G ARG 657": "NH1" <-> "NH2" Residue "G ARG 812": "NH1" <-> "NH2" Residue "H PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 203": "NH1" <-> "NH2" Residue "H ARG 211": "NH1" <-> "NH2" Residue "H ARG 241": "NH1" <-> "NH2" Residue "H ARG 297": "NH1" <-> "NH2" Residue "H ARG 324": "NH1" <-> "NH2" Residue "H ARG 357": "NH1" <-> "NH2" Residue "H ARG 387": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13861 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 619 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "B" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 3331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3331 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 403} Chain breaks: 4 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'UNK:plan-1': 41} Unresolved non-hydrogen planarities: 41 Chain: "H" Number of atoms: 3326 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 411, 3314 Classifications: {'peptide': 411} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'CIS': 3, 'PCIS': 3, 'PTRANS': 11, 'TRANS': 393} Chain breaks: 2 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'UNK:plan-1': 13} Unresolved non-hydrogen planarities: 29 Conformer: "B" Number of residues, atoms: 411, 3314 Classifications: {'peptide': 411} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'CIS': 3, 'PCIS': 3, 'PTRANS': 11, 'TRANS': 393} Chain breaks: 2 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'UNK:plan-1': 13} Unresolved non-hydrogen planarities: 29 bond proxies already assigned to first conformer: 3374 Chain: "I" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1466 Classifications: {'DNA': 72} Link IDs: {'rna3p': 71} Chain: "J" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1486 Classifications: {'DNA': 72} Link IDs: {'rna3p': 71} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ASER H 86 " occ=0.66 ... (10 atoms not shown) pdb=" OG BSER H 86 " occ=0.34 residue: pdb=" N ACYS H 207 " occ=0.61 ... (10 atoms not shown) pdb=" SG BCYS H 207 " occ=0.39 Time building chain proxies: 8.75, per 1000 atoms: 0.63 Number of scatterers: 13861 At special positions: 0 Unit cell: (95.4045, 120.659, 165.555, 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) S 44 16.00 P 144 15.00 O 2827 8.00 N 2497 7.00 C 8349 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.86 Conformation dependent library (CDL) restraints added in 2.4 seconds 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2576 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 16 sheets defined 39.6% alpha, 17.8% beta 65 base pairs and 102 stacking pairs defined. Time for finding SS restraints: 5.35 Creating SS restraints... Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.921A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA A 75 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLN A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.872A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N LEU A 103 " --> pdb=" O TYR A 99 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.650A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA A 127 " --> pdb=" O ASP A 123 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 48 through 77 removed outlier: 4.211A pdb=" N GLU B 52 " --> pdb=" O GLY B 48 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL B 57 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA B 69 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.970A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 38 removed outlier: 3.557A pdb=" N LYS C 36 " --> pdb=" O ARG C 32 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY C 37 " --> pdb=" O LEU C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 74 removed outlier: 4.137A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU C 51 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 87 Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.763A pdb=" N ASN D 67 " --> pdb=" O ASN D 63 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE D 69 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ARG D 72 " --> pdb=" O ASP D 68 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU D 76 " --> pdb=" O ARG D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.756A pdb=" N ALA D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 124 Processing helix chain 'E' and resid 44 through 57 removed outlier: 4.205A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 79 removed outlier: 4.191A pdb=" N LEU E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 115 removed outlier: 3.925A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU E 97 " --> pdb=" O GLN E 93 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU E 103 " --> pdb=" O TYR E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 132 removed outlier: 4.655A pdb=" N GLN E 125 " --> pdb=" O PRO E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.940A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.244A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE F 61 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 removed outlier: 3.685A pdb=" N VAL F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR F 88 " --> pdb=" O MET F 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 617 through 636 removed outlier: 4.396A pdb=" N ILE G 624 " --> pdb=" O ASN G 620 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE G 625 " --> pdb=" O ALA G 621 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LYS G 626 " --> pdb=" O PHE G 622 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLU G 627 " --> pdb=" O ARG G 623 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL G 628 " --> pdb=" O ILE G 624 " (cutoff:3.500A) Processing helix chain 'G' and resid 763 through 788 removed outlier: 3.635A pdb=" N GLN G 767 " --> pdb=" O LEU G 763 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS G 775 " --> pdb=" O GLU G 771 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU G 776 " --> pdb=" O MET G 772 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALA G 779 " --> pdb=" O LYS G 775 " (cutoff:3.500A) Processing helix chain 'G' and resid 878 through 890 Processing helix chain 'G' and resid 901 through 910 Processing helix chain 'G' and resid 916 through 924 removed outlier: 3.717A pdb=" N GLY G 920 " --> pdb=" O PHE G 917 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N GLY G 921 " --> pdb=" O GLU G 918 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N TRP G 922 " --> pdb=" O GLN G 919 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 90 removed outlier: 4.258A pdb=" N ASER H 86 " --> pdb=" O PHE H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 180 removed outlier: 3.549A pdb=" N UNK H 180 " --> pdb=" O UNK H 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 292 through 299 Processing helix chain 'H' and resid 309 through 323 removed outlier: 3.796A pdb=" N SER H 315 " --> pdb=" O TYR H 311 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL H 317 " --> pdb=" O MET H 313 " (cutoff:3.500A) Processing helix chain 'H' and resid 334 through 338 Processing helix chain 'H' and resid 407 through 421 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.269A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA3, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.917A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 530 through 532 removed outlier: 3.722A pdb=" N TYR G 530 " --> pdb=" O ILE G 539 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 554 through 562 removed outlier: 6.642A pdb=" N GLU G 597 " --> pdb=" O VAL H 163 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL H 163 " --> pdb=" O GLU G 597 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N THR G 599 " --> pdb=" O MET H 161 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL H 163 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR H 140 " --> pdb=" O THR H 147 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN H 138 " --> pdb=" O GLU H 149 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 698 through 700 removed outlier: 3.585A pdb=" N GLY G 686 " --> pdb=" O HIS G 683 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU G 665 " --> pdb=" O GLY G 678 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU G 680 " --> pdb=" O LYS G 663 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LYS G 663 " --> pdb=" O LEU G 680 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ALA G 682 " --> pdb=" O LYS G 661 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LYS G 661 " --> pdb=" O ALA G 682 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N ASP G 664 " --> pdb=" O GLU G 743 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N GLU G 743 " --> pdb=" O ASP G 664 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N ARG G 734 " --> pdb=" O ASN G 726 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N ASN G 726 " --> pdb=" O ARG G 734 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR G 736 " --> pdb=" O LEU G 724 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL G 738 " --> pdb=" O PHE G 722 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL G 719 " --> pdb=" O PHE G 709 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N PHE G 709 " --> pdb=" O VAL G 719 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N HIS G 721 " --> pdb=" O ALA G 707 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ALA G 707 " --> pdb=" O HIS G 721 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N HIS G 723 " --> pdb=" O LYS G 705 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 806 through 808 removed outlier: 3.501A pdb=" N PHE G 833 " --> pdb=" O ASN G 826 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 870 through 874 removed outlier: 6.770A pdb=" N MET G 870 " --> pdb=" O ILE G 859 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ILE G 859 " --> pdb=" O MET G 870 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ASN G 872 " --> pdb=" O MET G 857 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N MET G 857 " --> pdb=" O ASN G 872 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N THR G 894 " --> pdb=" O GLU G 841 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE G 843 " --> pdb=" O THR G 894 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.597A pdb=" N ASP H 75 " --> pdb=" O TYR H 11 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU H 62 " --> pdb=" O TYR H 74 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LYS H 63 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE H 52 " --> pdb=" O LYS H 63 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 111 through 114 removed outlier: 4.698A pdb=" N LEU H 119 " --> pdb=" O GLU H 130 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU H 130 " --> pdb=" O LEU H 119 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N PHE H 121 " --> pdb=" O VAL H 128 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 200 through 201 removed outlier: 3.676A pdb=" N CYS H 200 " --> pdb=" O ILE H 218 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 200 through 201 removed outlier: 3.676A pdb=" N CYS H 200 " --> pdb=" O ILE H 218 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 239 through 246 removed outlier: 6.507A pdb=" N SER H 258 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU H 242 " --> pdb=" O VAL H 256 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N VAL H 256 " --> pdb=" O LEU H 242 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LEU H 244 " --> pdb=" O PHE H 254 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N PHE H 254 " --> pdb=" O LEU H 244 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N GLN H 252 " --> pdb=" O PRO H 246 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N HIS H 271 " --> pdb=" O LEU H 259 " (cutoff:3.500A) removed outlier: 9.554A pdb=" N ARG H 269 " --> pdb=" O PRO H 261 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 342 through 344 Processing sheet with id=AB7, first strand: chain 'H' and resid 400 through 406 removed outlier: 6.520A pdb=" N PHE H 389 " --> pdb=" O SER H 405 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LYS H 426 " --> pdb=" O SER H 375 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL H 377 " --> pdb=" O LYS H 426 " (cutoff:3.500A) 439 hydrogen bonds defined for protein. 1240 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 152 hydrogen bonds 244 hydrogen bond angles 0 basepair planarities 65 basepair parallelities 102 stacking parallelities Total time for adding SS restraints: 6.19 Time building geometry restraints manager: 6.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3386 1.33 - 1.45: 3635 1.45 - 1.57: 7041 1.57 - 1.70: 286 1.70 - 1.82: 73 Bond restraints: 14421 Sorted by residual: bond pdb=" CA GLU H 299 " pdb=" C GLU H 299 " ideal model delta sigma weight residual 1.523 1.558 -0.034 1.34e-02 5.57e+03 6.56e+00 bond pdb=" N ASP H 101 " pdb=" CA ASP H 101 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.90e-02 2.77e+03 4.58e+00 bond pdb=" C TYR H 93 " pdb=" N ARG H 94 " ideal model delta sigma weight residual 1.333 1.306 0.028 1.43e-02 4.89e+03 3.74e+00 bond pdb=" C LYS H 100 " pdb=" N ASP H 101 " ideal model delta sigma weight residual 1.329 1.354 -0.025 1.40e-02 5.10e+03 3.29e+00 bond pdb=" N GLU H 299 " pdb=" CA GLU H 299 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.29e-02 6.01e+03 3.13e+00 ... (remaining 14416 not shown) Histogram of bond angle deviations from ideal: 98.05 - 105.24: 749 105.24 - 112.43: 7552 112.43 - 119.62: 4677 119.62 - 126.81: 6616 126.81 - 134.01: 482 Bond angle restraints: 20076 Sorted by residual: angle pdb=" N TYR H 93 " pdb=" CA TYR H 93 " pdb=" C TYR H 93 " ideal model delta sigma weight residual 111.75 122.51 -10.76 1.28e+00 6.10e-01 7.07e+01 angle pdb=" N ILE G 586 " pdb=" CA ILE G 586 " pdb=" C ILE G 586 " ideal model delta sigma weight residual 111.91 105.33 6.58 8.90e-01 1.26e+00 5.46e+01 angle pdb=" N THR H 170 " pdb=" CA THR H 170 " pdb=" C THR H 170 " ideal model delta sigma weight residual 111.28 102.21 9.07 1.35e+00 5.49e-01 4.51e+01 angle pdb=" N TYR E 41 " pdb=" CA TYR E 41 " pdb=" C TYR E 41 " ideal model delta sigma weight residual 110.50 119.93 -9.43 1.41e+00 5.03e-01 4.47e+01 angle pdb=" C LYS H 100 " pdb=" N ASP H 101 " pdb=" CA ASP H 101 " ideal model delta sigma weight residual 121.70 132.96 -11.26 1.80e+00 3.09e-01 3.91e+01 ... (remaining 20071 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.34: 7395 27.34 - 54.68: 769 54.68 - 82.01: 148 82.01 - 109.35: 3 109.35 - 136.69: 2 Dihedral angle restraints: 8317 sinusoidal: 4331 harmonic: 3986 Sorted by residual: dihedral pdb=" CA PHE H 165 " pdb=" C PHE H 165 " pdb=" N TYR H 166 " pdb=" CA TYR H 166 " ideal model delta harmonic sigma weight residual 180.00 151.69 28.31 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA TYR H 11 " pdb=" C TYR H 11 " pdb=" N GLN H 12 " pdb=" CA GLN H 12 " ideal model delta harmonic sigma weight residual 180.00 152.04 27.96 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA PHE H 89 " pdb=" C PHE H 89 " pdb=" N LYS H 90 " pdb=" CA LYS H 90 " ideal model delta harmonic sigma weight residual -180.00 -152.38 -27.62 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 8314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 2085 0.097 - 0.193: 152 0.193 - 0.290: 8 0.290 - 0.386: 2 0.386 - 0.482: 2 Chirality restraints: 2249 Sorted by residual: chirality pdb=" CB VAL H 362 " pdb=" CA VAL H 362 " pdb=" CG1 VAL H 362 " pdb=" CG2 VAL H 362 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.82e+00 chirality pdb=" CA TYR H 93 " pdb=" N TYR H 93 " pdb=" C TYR H 93 " pdb=" CB TYR H 93 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" CB ILE G 718 " pdb=" CA ILE G 718 " pdb=" CG1 ILE G 718 " pdb=" CG2 ILE G 718 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.24e+00 ... (remaining 2246 not shown) Planarity restraints: 2064 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL H 167 " -0.020 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C VAL H 167 " 0.070 2.00e-02 2.50e+03 pdb=" O VAL H 167 " -0.026 2.00e-02 2.50e+03 pdb=" N PRO H 168 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS H 92 " -0.018 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C HIS H 92 " 0.064 2.00e-02 2.50e+03 pdb=" O HIS H 92 " -0.024 2.00e-02 2.50e+03 pdb=" N TYR H 93 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 40 " -0.023 2.00e-02 2.50e+03 1.88e-02 7.10e+00 pdb=" CG TYR D 40 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR D 40 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR D 40 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR D 40 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR D 40 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR D 40 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR D 40 " -0.000 2.00e-02 2.50e+03 ... (remaining 2061 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.24: 27 2.24 - 2.90: 5238 2.90 - 3.57: 21762 3.57 - 4.23: 36645 4.23 - 4.90: 54899 Nonbonded interactions: 118571 Sorted by model distance: nonbonded pdb=" NZ LYS G 626 " pdb=" OP1 DT I -6 " model vdw 1.570 2.520 nonbonded pdb=" NE2 GLN H 267 " pdb=" OP1 DC J 1 " model vdw 1.571 2.520 nonbonded pdb=" CG GLN H 267 " pdb=" OP1 DC J 1 " model vdw 1.687 3.440 nonbonded pdb=" NH1 ARG E 40 " pdb=" N2 DG J -8 " model vdw 1.734 3.200 nonbonded pdb=" CD GLN H 267 " pdb=" OP1 DC J 1 " model vdw 1.833 3.270 ... (remaining 118566 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 'B' selection = (chain 'F' and resid 25 through 102) } 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=0.32 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: 0.330 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: 2.410 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 44.960 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 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 0.076 14421 Z= 0.343 Angle : 0.939 11.256 20076 Z= 0.553 Chirality : 0.053 0.482 2249 Planarity : 0.007 0.064 2064 Dihedral : 20.419 136.691 5741 Min Nonbonded Distance : 1.570 Molprobity Statistics. All-atom Clashscore : 20.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.24 % 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: -3.94 (0.19), residues: 1292 helix: -2.50 (0.17), residues: 446 sheet: -3.00 (0.34), residues: 169 loop : -2.58 (0.20), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP G 902 HIS 0.009 0.002 HIS H 247 PHE 0.037 0.003 PHE H 222 TYR 0.046 0.004 TYR D 40 ARG 0.013 0.001 ARG D 79 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.9866 (mt-10) cc_final: 0.9598 (mp0) REVERT: A 99 TYR cc_start: 0.9380 (t80) cc_final: 0.8876 (t80) REVERT: A 129 ARG cc_start: 0.9575 (mtt180) cc_final: 0.9007 (ttm110) REVERT: B 50 ILE cc_start: 0.9300 (mm) cc_final: 0.8840 (mm) REVERT: B 61 PHE cc_start: 0.9595 (t80) cc_final: 0.9338 (t80) REVERT: B 68 ASP cc_start: 0.9072 (p0) cc_final: 0.8815 (p0) REVERT: D 37 TYR cc_start: 0.9109 (m-80) cc_final: 0.8849 (m-80) REVERT: D 82 HIS cc_start: 0.9774 (t-90) cc_final: 0.9521 (m90) REVERT: E 67 PHE cc_start: 0.9506 (t80) cc_final: 0.9134 (t80) REVERT: E 94 GLU cc_start: 0.9712 (tp30) cc_final: 0.9452 (tt0) REVERT: F 84 MET cc_start: 0.9609 (mmp) cc_final: 0.9406 (mpp) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.3081 time to fit residues: 57.9478 Evaluate side-chains 91 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 61 optimal weight: 20.0000 chunk 38 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 70 optimal weight: 7.9990 chunk 85 optimal weight: 20.0000 chunk 133 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN B 64 ASN ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN F 25 ASN G 585 ASN G 604 ASN G 619 GLN ** G 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 739 GLN H 12 GLN ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 144 ASN ** H 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 290 ASN ** H 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 14421 Z= 0.347 Angle : 0.775 10.920 20076 Z= 0.434 Chirality : 0.044 0.243 2249 Planarity : 0.007 0.067 2064 Dihedral : 26.389 145.164 3075 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 35.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 0.26 % Allowed : 2.70 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.21), residues: 1292 helix: -1.11 (0.21), residues: 470 sheet: -2.68 (0.38), residues: 151 loop : -2.30 (0.22), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP G 902 HIS 0.010 0.002 HIS F 75 PHE 0.018 0.002 PHE H 403 TYR 0.027 0.003 TYR C 50 ARG 0.012 0.001 ARG F 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 109 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.9445 (t80) cc_final: 0.8870 (t80) REVERT: A 110 CYS cc_start: 0.9360 (m) cc_final: 0.9027 (m) REVERT: B 68 ASP cc_start: 0.8760 (p0) cc_final: 0.8397 (p0) REVERT: D 82 HIS cc_start: 0.9822 (t-90) cc_final: 0.9586 (m90) REVERT: E 62 ILE cc_start: 0.9385 (mm) cc_final: 0.9160 (mm) REVERT: E 93 GLN cc_start: 0.9679 (tt0) cc_final: 0.9225 (tp40) REVERT: E 94 GLU cc_start: 0.9789 (tp30) cc_final: 0.9581 (tt0) REVERT: H 253 MET cc_start: 0.9052 (mmp) cc_final: 0.8385 (mtt) outliers start: 3 outliers final: 3 residues processed: 112 average time/residue: 0.3277 time to fit residues: 52.8552 Evaluate side-chains 86 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 83 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 74 optimal weight: 7.9990 chunk 41 optimal weight: 20.0000 chunk 111 optimal weight: 4.9990 chunk 90 optimal weight: 40.0000 chunk 36 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 710 GLN G 723 HIS ** G 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 739 GLN ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 14421 Z= 0.329 Angle : 0.737 10.173 20076 Z= 0.416 Chirality : 0.043 0.254 2249 Planarity : 0.006 0.065 2064 Dihedral : 26.997 142.727 3075 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 37.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 0.35 % Allowed : 2.61 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.57 (0.22), residues: 1292 helix: -0.71 (0.22), residues: 476 sheet: -2.63 (0.36), residues: 169 loop : -2.21 (0.23), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP G 902 HIS 0.010 0.002 HIS H 224 PHE 0.017 0.002 PHE H 403 TYR 0.023 0.003 TYR D 37 ARG 0.009 0.001 ARG G 569 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.9532 (t80) cc_final: 0.9059 (t80) REVERT: D 102 LEU cc_start: 0.9419 (tp) cc_final: 0.9217 (tp) REVERT: E 93 GLN cc_start: 0.9729 (tt0) cc_final: 0.9368 (tt0) REVERT: E 94 GLU cc_start: 0.9821 (tp30) cc_final: 0.9614 (tt0) REVERT: H 253 MET cc_start: 0.9035 (mmp) cc_final: 0.8414 (mtt) REVERT: H 289 MET cc_start: 0.8620 (mpp) cc_final: 0.8327 (mpp) REVERT: H 313 MET cc_start: 0.9211 (ttm) cc_final: 0.8878 (mtp) outliers start: 4 outliers final: 2 residues processed: 104 average time/residue: 0.3044 time to fit residues: 44.8213 Evaluate side-chains 76 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 74 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 132 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 14 optimal weight: 20.0000 chunk 63 optimal weight: 7.9990 chunk 89 optimal weight: 50.0000 chunk 134 optimal weight: 8.9990 chunk 142 optimal weight: 6.9990 chunk 70 optimal weight: 20.0000 chunk 127 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 739 GLN ** G 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 152 GLN ** H 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 14421 Z= 0.354 Angle : 0.752 11.600 20076 Z= 0.423 Chirality : 0.044 0.238 2249 Planarity : 0.006 0.066 2064 Dihedral : 27.513 144.724 3075 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 42.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.63 (0.21), residues: 1292 helix: -0.81 (0.21), residues: 484 sheet: -2.71 (0.36), residues: 167 loop : -2.21 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP G 902 HIS 0.010 0.002 HIS H 224 PHE 0.019 0.002 PHE H 150 TYR 0.023 0.003 TYR D 37 ARG 0.016 0.001 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.9885 (mt-10) cc_final: 0.9661 (mm-30) REVERT: D 99 ARG cc_start: 0.8841 (mmt180) cc_final: 0.8327 (mtt-85) REVERT: E 93 GLN cc_start: 0.9773 (tt0) cc_final: 0.9389 (tt0) REVERT: E 94 GLU cc_start: 0.9824 (tp30) cc_final: 0.9498 (tm-30) REVERT: E 110 CYS cc_start: 0.9575 (m) cc_final: 0.9361 (m) REVERT: F 84 MET cc_start: 0.9723 (mpp) cc_final: 0.9491 (mpp) REVERT: F 97 LEU cc_start: 0.9515 (mt) cc_final: 0.8843 (mt) REVERT: H 253 MET cc_start: 0.9080 (mmp) cc_final: 0.8561 (mtt) REVERT: H 289 MET cc_start: 0.8659 (mpp) cc_final: 0.8338 (mpp) REVERT: H 313 MET cc_start: 0.9231 (ttm) cc_final: 0.8813 (mtp) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.3095 time to fit residues: 39.4260 Evaluate side-chains 70 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 118 optimal weight: 4.9990 chunk 80 optimal weight: 20.0000 chunk 2 optimal weight: 6.9990 chunk 105 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 chunk 121 optimal weight: 7.9990 chunk 98 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 72 optimal weight: 50.0000 chunk 127 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 739 GLN ** G 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 ASN H 152 GLN ** H 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 14421 Z= 0.298 Angle : 0.693 9.717 20076 Z= 0.394 Chirality : 0.042 0.207 2249 Planarity : 0.005 0.068 2064 Dihedral : 27.599 142.425 3075 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 38.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.21), residues: 1292 helix: -0.49 (0.22), residues: 475 sheet: -2.62 (0.36), residues: 167 loop : -2.14 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP G 922 HIS 0.008 0.001 HIS H 224 PHE 0.017 0.002 PHE H 403 TYR 0.036 0.003 TYR B 88 ARG 0.006 0.001 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 TYR cc_start: 0.8962 (m-80) cc_final: 0.8724 (m-10) REVERT: E 93 GLN cc_start: 0.9747 (tt0) cc_final: 0.9430 (tt0) REVERT: E 94 GLU cc_start: 0.9833 (tp30) cc_final: 0.9515 (tm-30) REVERT: F 84 MET cc_start: 0.9722 (mpp) cc_final: 0.9446 (mpp) REVERT: F 97 LEU cc_start: 0.9557 (mt) cc_final: 0.8919 (mt) REVERT: H 253 MET cc_start: 0.9088 (mmp) cc_final: 0.8596 (mtt) REVERT: H 289 MET cc_start: 0.8580 (mpp) cc_final: 0.8340 (mpp) REVERT: H 313 MET cc_start: 0.9258 (ttm) cc_final: 0.8803 (mtp) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.3132 time to fit residues: 41.6060 Evaluate side-chains 69 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 47 optimal weight: 0.0670 chunk 127 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 142 optimal weight: 7.9990 chunk 118 optimal weight: 10.0000 chunk 65 optimal weight: 50.0000 chunk 11 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 137 optimal weight: 7.9990 overall best weight: 2.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 673 GLN ** G 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 739 GLN H 60 HIS H 108 ASN H 265 GLN ** H 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14421 Z= 0.194 Angle : 0.606 9.058 20076 Z= 0.345 Chirality : 0.040 0.198 2249 Planarity : 0.004 0.067 2064 Dihedral : 27.408 140.632 3075 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 27.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.22), residues: 1292 helix: 0.15 (0.23), residues: 479 sheet: -2.26 (0.37), residues: 163 loop : -2.00 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 922 HIS 0.006 0.001 HIS H 224 PHE 0.011 0.001 PHE A 104 TYR 0.024 0.002 TYR B 88 ARG 0.005 0.001 ARG G 569 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 TYR cc_start: 0.8989 (m-80) cc_final: 0.8713 (m-10) REVERT: E 67 PHE cc_start: 0.9293 (t80) cc_final: 0.8538 (t80) REVERT: E 93 GLN cc_start: 0.9787 (tt0) cc_final: 0.9456 (tt0) REVERT: F 84 MET cc_start: 0.9690 (mpp) cc_final: 0.9465 (mpp) REVERT: H 253 MET cc_start: 0.9082 (mmp) cc_final: 0.8590 (mtt) REVERT: H 289 MET cc_start: 0.8646 (mpp) cc_final: 0.8396 (mpp) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.2878 time to fit residues: 44.4958 Evaluate side-chains 77 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 16 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 80 optimal weight: 20.0000 chunk 119 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 141 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 86 optimal weight: 0.0770 chunk 65 optimal weight: 50.0000 chunk 87 optimal weight: 5.9990 overall best weight: 4.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 723 HIS G 739 GLN G 849 GLN ** H 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.5171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14421 Z= 0.246 Angle : 0.641 8.503 20076 Z= 0.364 Chirality : 0.041 0.195 2249 Planarity : 0.005 0.066 2064 Dihedral : 27.418 140.860 3075 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 33.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 0.09 % Allowed : 1.48 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.22), residues: 1292 helix: 0.23 (0.23), residues: 468 sheet: -2.30 (0.36), residues: 173 loop : -1.99 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 922 HIS 0.008 0.001 HIS H 224 PHE 0.015 0.002 PHE H 150 TYR 0.020 0.002 TYR B 72 ARG 0.006 0.001 ARG G 569 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 100 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 CYS cc_start: 0.9540 (m) cc_final: 0.9294 (m) REVERT: A 122 LYS cc_start: 0.9665 (ttpt) cc_final: 0.9460 (ptmt) REVERT: A 126 LEU cc_start: 0.9824 (tp) cc_final: 0.9608 (pp) REVERT: B 72 TYR cc_start: 0.9004 (m-80) cc_final: 0.8743 (m-10) REVERT: D 59 MET cc_start: 0.9560 (ttm) cc_final: 0.9312 (mtt) REVERT: E 67 PHE cc_start: 0.9310 (t80) cc_final: 0.8646 (t80) REVERT: E 93 GLN cc_start: 0.9747 (tt0) cc_final: 0.9475 (tt0) REVERT: E 94 GLU cc_start: 0.9730 (tt0) cc_final: 0.9403 (pt0) REVERT: E 110 CYS cc_start: 0.9490 (m) cc_final: 0.9266 (m) REVERT: F 84 MET cc_start: 0.9702 (mpp) cc_final: 0.9439 (mpp) REVERT: G 559 MET cc_start: 0.8872 (tmm) cc_final: 0.8353 (tmm) REVERT: G 849 GLN cc_start: 0.7184 (OUTLIER) cc_final: 0.6839 (tm-30) REVERT: H 253 MET cc_start: 0.9090 (mmp) cc_final: 0.8551 (mtt) REVERT: H 313 MET cc_start: 0.9140 (ttm) cc_final: 0.8763 (mtp) outliers start: 1 outliers final: 0 residues processed: 101 average time/residue: 0.2953 time to fit residues: 43.3444 Evaluate side-chains 76 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 56 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 90 optimal weight: 40.0000 chunk 96 optimal weight: 0.0060 chunk 70 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 chunk 128 optimal weight: 8.9990 chunk 135 optimal weight: 8.9990 overall best weight: 3.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 739 GLN H 265 GLN ** H 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.5267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14421 Z= 0.213 Angle : 0.613 7.728 20076 Z= 0.350 Chirality : 0.040 0.191 2249 Planarity : 0.004 0.067 2064 Dihedral : 27.398 140.420 3075 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 28.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.23), residues: 1292 helix: 0.43 (0.24), residues: 471 sheet: -2.17 (0.36), residues: 173 loop : -1.93 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 922 HIS 0.005 0.001 HIS H 224 PHE 0.011 0.002 PHE H 403 TYR 0.022 0.002 TYR B 72 ARG 0.005 0.001 ARG G 569 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 CYS cc_start: 0.9531 (m) cc_final: 0.9253 (m) REVERT: A 122 LYS cc_start: 0.9659 (ttpt) cc_final: 0.9448 (ptmt) REVERT: A 126 LEU cc_start: 0.9808 (tp) cc_final: 0.9607 (pp) REVERT: B 72 TYR cc_start: 0.9000 (m-80) cc_final: 0.8750 (m-10) REVERT: D 59 MET cc_start: 0.9567 (ttm) cc_final: 0.9294 (mtt) REVERT: E 67 PHE cc_start: 0.9292 (t80) cc_final: 0.8613 (t80) REVERT: E 93 GLN cc_start: 0.9746 (tt0) cc_final: 0.9425 (tp40) REVERT: E 110 CYS cc_start: 0.9495 (m) cc_final: 0.9261 (m) REVERT: G 559 MET cc_start: 0.8860 (tmm) cc_final: 0.8477 (tmm) REVERT: H 253 MET cc_start: 0.9112 (mmp) cc_final: 0.8638 (mtt) REVERT: H 289 MET cc_start: 0.8719 (mpp) cc_final: 0.8408 (mpp) REVERT: H 313 MET cc_start: 0.9153 (ttm) cc_final: 0.8770 (mtp) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.2960 time to fit residues: 43.3032 Evaluate side-chains 74 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 135 optimal weight: 8.9990 chunk 79 optimal weight: 0.0970 chunk 57 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 131 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 overall best weight: 5.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 739 GLN ** H 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.5575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14421 Z= 0.276 Angle : 0.669 8.328 20076 Z= 0.380 Chirality : 0.042 0.191 2249 Planarity : 0.005 0.067 2064 Dihedral : 27.534 140.920 3075 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 36.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.22), residues: 1292 helix: 0.21 (0.23), residues: 469 sheet: -2.10 (0.38), residues: 173 loop : -1.97 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 922 HIS 0.009 0.001 HIS H 224 PHE 0.016 0.002 PHE H 150 TYR 0.021 0.002 TYR B 72 ARG 0.007 0.001 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 CYS cc_start: 0.9539 (m) cc_final: 0.9262 (m) REVERT: A 122 LYS cc_start: 0.9656 (ttpt) cc_final: 0.9426 (ptmt) REVERT: A 134 ARG cc_start: 0.9350 (tpp-160) cc_final: 0.9028 (mmm160) REVERT: D 59 MET cc_start: 0.9563 (ttm) cc_final: 0.9276 (mtt) REVERT: D 99 ARG cc_start: 0.8891 (mmt180) cc_final: 0.8387 (mtt-85) REVERT: E 67 PHE cc_start: 0.9275 (t80) cc_final: 0.8662 (t80) REVERT: E 93 GLN cc_start: 0.9720 (tt0) cc_final: 0.9416 (tp40) REVERT: E 110 CYS cc_start: 0.9541 (m) cc_final: 0.9281 (m) REVERT: F 84 MET cc_start: 0.9709 (mpp) cc_final: 0.9499 (mpp) REVERT: G 559 MET cc_start: 0.8866 (tmm) cc_final: 0.8468 (tmm) REVERT: H 253 MET cc_start: 0.9108 (mmp) cc_final: 0.8627 (mtt) REVERT: H 289 MET cc_start: 0.8462 (mpp) cc_final: 0.8123 (mpp) REVERT: H 313 MET cc_start: 0.9113 (ttm) cc_final: 0.8829 (mtp) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.3064 time to fit residues: 43.1362 Evaluate side-chains 75 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 139 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 66 optimal weight: 30.0000 chunk 97 optimal weight: 8.9990 chunk 146 optimal weight: 8.9990 chunk 134 optimal weight: 8.9990 chunk 116 optimal weight: 20.0000 chunk 12 optimal weight: 2.9990 chunk 90 optimal weight: 40.0000 chunk 71 optimal weight: 6.9990 chunk 92 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 739 GLN ** G 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.6029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 14421 Z= 0.386 Angle : 0.782 9.343 20076 Z= 0.441 Chirality : 0.045 0.205 2249 Planarity : 0.006 0.064 2064 Dihedral : 27.945 141.817 3075 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 47.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.26 (0.22), residues: 1292 helix: -0.41 (0.22), residues: 469 sheet: -2.34 (0.40), residues: 156 loop : -2.12 (0.22), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP G 902 HIS 0.012 0.002 HIS H 224 PHE 0.019 0.002 PHE H 389 TYR 0.022 0.003 TYR H 401 ARG 0.009 0.001 ARG H 408 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 99 ARG cc_start: 0.8949 (mmt180) cc_final: 0.8457 (mtt-85) REVERT: E 67 PHE cc_start: 0.9342 (t80) cc_final: 0.8853 (t80) REVERT: F 88 TYR cc_start: 0.9879 (m-80) cc_final: 0.9657 (m-80) REVERT: H 18 MET cc_start: 0.7570 (mmt) cc_final: 0.7268 (mmm) REVERT: H 253 MET cc_start: 0.8986 (mmp) cc_final: 0.8558 (mtt) REVERT: H 313 MET cc_start: 0.9123 (ttm) cc_final: 0.8857 (mtp) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.3035 time to fit residues: 38.2795 Evaluate side-chains 65 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 107 optimal weight: 0.1980 chunk 17 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 48 optimal weight: 0.5980 chunk 119 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 739 GLN H 265 GLN ** H 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.031969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2334 r_free = 0.2334 target = 0.019698 restraints weight = 449498.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2400 r_free = 0.2400 target = 0.021128 restraints weight = 198595.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2444 r_free = 0.2444 target = 0.022119 restraints weight = 117159.875| |-----------------------------------------------------------------------------| r_work (final): 0.2410 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2386 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2386 r_free = 0.2386 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2383 r_free = 0.2383 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.5778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14421 Z= 0.186 Angle : 0.618 7.489 20076 Z= 0.350 Chirality : 0.041 0.183 2249 Planarity : 0.004 0.071 2064 Dihedral : 27.678 138.292 3075 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 25.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.23), residues: 1292 helix: 0.42 (0.24), residues: 478 sheet: -1.96 (0.37), residues: 186 loop : -1.88 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 922 HIS 0.005 0.001 HIS H 224 PHE 0.015 0.002 PHE B 61 TYR 0.019 0.002 TYR B 88 ARG 0.009 0.001 ARG B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2274.65 seconds wall clock time: 42 minutes 35.51 seconds (2555.51 seconds total)