Starting phenix.real_space_refine on Mon Mar 18 10:26:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zit_11229/03_2024/6zit_11229_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zit_11229/03_2024/6zit_11229.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zit_11229/03_2024/6zit_11229.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zit_11229/03_2024/6zit_11229.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zit_11229/03_2024/6zit_11229_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zit_11229/03_2024/6zit_11229_trim_updated.pdb" } resolution = 3.49 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= 0.001 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 53 5.16 5 C 6644 2.51 5 N 1684 2.21 5 O 1819 1.98 5 H 10446 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "8 ASP 5": "OD1" <-> "OD2" Residue "8 PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 3": "OE1" <-> "OE2" Residue "a PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ARG 36": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ARG 159": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ASP 224": "OD1" <-> "OD2" Residue "d ASP 52": "OD1" <-> "OD2" Residue "d TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d ASP 83": "OD1" <-> "OD2" Residue "d TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d GLU 117": "OE1" <-> "OE2" Residue "d GLU 137": "OE1" <-> "OE2" Residue "d ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "e TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f ARG 73": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f GLU 77": "OE1" <-> "OE2" Residue "f GLU 81": "OE1" <-> "OE2" Residue "f ARG 84": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g ARG 25": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "j TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j ASP 42": "OD1" <-> "OD2" Residue "R ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R GLU 58": "OE1" <-> "OE2" Residue "K PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 56": "OE1" <-> "OE2" Residue "b GLU 80": "OE1" <-> "OE2" Residue "b GLU 95": "OE1" <-> "OE2" Residue "b ASP 106": "OD1" <-> "OD2" Residue "b ARG 121": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 141": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b GLU 190": "OE1" <-> "OE2" Residue "h PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S ASP 127": "OD1" <-> "OD2" Residue "S ARG 165": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 14": "OE1" <-> "OE2" Residue "C ASP 20": "OD1" <-> "OD2" Residue "C ASP 36": "OD1" <-> "OD2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 79": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20646 Number of models: 1 Model: "" Number of chains: 15 Chain: "8" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 649 Classifications: {'peptide': 38} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain: "a" Number of atoms: 3611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3611 Classifications: {'peptide': 226} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 213} Chain: "d" Number of atoms: 2534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 2534 Classifications: {'peptide': 154} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 142} Chain: "e" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 687 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 3, 'TRANS': 37} Chain: "f" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1411 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "g" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1291 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "j" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 828 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "k" Number of atoms: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 257 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'TYR:plan': 4, 'PHE:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 56 Chain: "R" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 839 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 855 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 487 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "b" Number of atoms: 3457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3457 Classifications: {'peptide': 209} Modifications used: {'NH2': 1} Link IDs: {'PTRANS': 7, 'TRANS': 201} Chain: "h" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1009 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 5, 'TRANS': 56} Chain: "S" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1398 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "C" Number of atoms: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1333 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Time building chain proxies: 9.15, per 1000 atoms: 0.44 Number of scatterers: 20646 At special positions: 0 Unit cell: (94.32, 124.712, 246.28, 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 53 16.00 O 1819 8.00 N 1684 7.00 C 6644 6.00 H 10446 1.00 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: 15.91 Conformation dependent library (CDL) restraints added in 2.0 seconds 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2440 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 4 sheets defined 69.0% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.87 Creating SS restraints... Processing helix chain '8' and resid 6 through 28 removed outlier: 5.212A pdb=" N LEU 8 10 " --> pdb=" O SER 8 7 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU 8 14 " --> pdb=" O THR 8 11 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU 8 18 " --> pdb=" O SER 8 15 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE 8 21 " --> pdb=" O LEU 8 18 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE 8 22 " --> pdb=" O THR 8 19 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ILE 8 23 " --> pdb=" O LEU 8 20 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N PHE 8 24 " --> pdb=" O PHE 8 21 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLN 8 25 " --> pdb=" O ILE 8 22 " (cutoff:3.500A) Processing helix chain 'a' and resid 7 through 9 No H-bonds generated for 'chain 'a' and resid 7 through 9' Processing helix chain 'a' and resid 19 through 30 removed outlier: 3.714A pdb=" N PHE a 26 " --> pdb=" O ILE a 23 " (cutoff:3.500A) Proline residue: a 27 - end of helix Processing helix chain 'a' and resid 41 through 60 removed outlier: 3.769A pdb=" N SER a 59 " --> pdb=" O LYS a 55 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ILE a 60 " --> pdb=" O GLN a 56 " (cutoff:3.500A) Processing helix chain 'a' and resid 63 through 87 removed outlier: 5.310A pdb=" N LEU a 70 " --> pdb=" O GLN a 66 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N MET a 71 " --> pdb=" O THR a 67 " (cutoff:3.500A) Processing helix chain 'a' and resid 94 through 96 No H-bonds generated for 'chain 'a' and resid 94 through 96' Processing helix chain 'a' and resid 98 through 119 Proline residue: a 107 - end of helix Processing helix chain 'a' and resid 121 through 128 Processing helix chain 'a' and resid 135 through 183 Proline residue: a 139 - end of helix removed outlier: 3.939A pdb=" N ILE a 143 " --> pdb=" O MET a 140 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR a 146 " --> pdb=" O ILE a 143 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN a 152 " --> pdb=" O LEU a 149 " (cutoff:3.500A) Proline residue: a 153 - end of helix removed outlier: 4.693A pdb=" N ALA a 166 " --> pdb=" O ASN a 163 " (cutoff:3.500A) Processing helix chain 'a' and resid 187 through 224 Processing helix chain 'd' and resid 12 through 18 removed outlier: 4.253A pdb=" N GLU d 17 " --> pdb=" O VAL d 13 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE d 18 " --> pdb=" O ALA d 14 " (cutoff:3.500A) Processing helix chain 'd' and resid 21 through 43 removed outlier: 5.057A pdb=" N ALA d 25 " --> pdb=" O ASN d 22 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL d 26 " --> pdb=" O GLN d 23 " (cutoff:3.500A) Processing helix chain 'd' and resid 53 through 59 Processing helix chain 'd' and resid 63 through 75 Processing helix chain 'd' and resid 86 through 100 removed outlier: 3.748A pdb=" N CYS d 100 " --> pdb=" O VAL d 97 " (cutoff:3.500A) Processing helix chain 'd' and resid 105 through 122 Processing helix chain 'd' and resid 127 through 129 No H-bonds generated for 'chain 'd' and resid 127 through 129' Processing helix chain 'd' and resid 132 through 138 Processing helix chain 'd' and resid 140 through 142 No H-bonds generated for 'chain 'd' and resid 140 through 142' Processing helix chain 'e' and resid 8 through 41 Proline residue: e 34 - end of helix Processing helix chain 'f' and resid 11 through 13 No H-bonds generated for 'chain 'f' and resid 11 through 13' Processing helix chain 'f' and resid 16 through 25 Proline residue: f 20 - end of helix removed outlier: 3.576A pdb=" N LEU f 24 " --> pdb=" O PRO f 20 " (cutoff:3.500A) Processing helix chain 'f' and resid 30 through 48 Processing helix chain 'f' and resid 56 through 79 removed outlier: 4.203A pdb=" N SER f 60 " --> pdb=" O ALA f 57 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N MET f 61 " --> pdb=" O GLY f 58 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LYS f 76 " --> pdb=" O ARG f 73 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 33 Processing helix chain 'g' and resid 42 through 60 Proline residue: g 46 - end of helix Processing helix chain 'g' and resid 63 through 66 Processing helix chain 'g' and resid 69 through 93 removed outlier: 3.760A pdb=" N TRP g 85 " --> pdb=" O GLU g 81 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N PHE g 86 " --> pdb=" O VAL g 82 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR g 87 " --> pdb=" O TRP g 83 " (cutoff:3.500A) Processing helix chain 'j' and resid 3 through 9 Processing helix chain 'j' and resid 14 through 18 Processing helix chain 'j' and resid 22 through 47 removed outlier: 3.685A pdb=" N ALA j 47 " --> pdb=" O LYS j 43 " (cutoff:3.500A) Processing helix chain 'k' and resid 16 through 18 No H-bonds generated for 'chain 'k' and resid 16 through 18' Processing helix chain 'k' and resid 23 through 44 Processing helix chain 'R' and resid 20 through 38 Processing helix chain 'R' and resid 45 through 73 Processing helix chain 'K' and resid 20 through 37 Processing helix chain 'K' and resid 45 through 72 Processing helix chain 'L' and resid 45 through 73 removed outlier: 3.559A pdb=" N ILE L 71 " --> pdb=" O VAL L 67 " (cutoff:3.500A) Processing helix chain 'b' and resid 20 through 29 Proline residue: b 27 - end of helix Processing helix chain 'b' and resid 33 through 48 Processing helix chain 'b' and resid 55 through 186 removed outlier: 6.087A pdb=" N ALA b 76 " --> pdb=" O LYS b 72 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N SER b 77 " --> pdb=" O LYS b 73 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N HIS b 122 " --> pdb=" O VAL b 118 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N TYR b 123 " --> pdb=" O GLN b 119 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LEU b 124 " --> pdb=" O LYS b 120 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N PHE b 125 " --> pdb=" O ARG b 121 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG b 129 " --> pdb=" O PHE b 125 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N HIS b 158 " --> pdb=" O ARG b 154 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE b 159 " --> pdb=" O LEU b 155 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL b 161 " --> pdb=" O TYR b 157 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N SER b 186 " --> pdb=" O VAL b 182 " (cutoff:3.500A) Processing helix chain 'b' and resid 190 through 208 Processing helix chain 'h' and resid 9 through 26 removed outlier: 4.066A pdb=" N GLY h 26 " --> pdb=" O ARG h 22 " (cutoff:3.500A) Processing helix chain 'h' and resid 33 through 50 Processing helix chain 'S' and resid 101 through 112 Processing helix chain 'S' and resid 128 through 141 Processing helix chain 'S' and resid 175 through 186 Processing helix chain 'C' and resid 7 through 17 Processing sheet with id= A, first strand: chain 'S' and resid 115 through 117 removed outlier: 6.500A pdb=" N VAL S 147 " --> pdb=" O VAL S 116 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'S' and resid 152 through 154 removed outlier: 7.158A pdb=" N LYS S 153 " --> pdb=" O CYS S 118 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL S 120 " --> pdb=" O LYS S 153 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 71 through 74 removed outlier: 6.276A pdb=" N HIS C 42 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL C 31 " --> pdb=" O HIS C 42 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 51 through 53 674 hydrogen bonds defined for protein. 1665 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: 7.11 Time building geometry restraints manager: 16.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10439 1.03 - 1.23: 40 1.23 - 1.42: 4146 1.42 - 1.62: 6126 1.62 - 1.81: 99 Bond restraints: 20850 Sorted by residual: bond pdb=" CB MET j 31 " pdb=" CG MET j 31 " ideal model delta sigma weight residual 1.520 1.452 0.068 3.00e-02 1.11e+03 5.17e+00 bond pdb=" CB PRO f 5 " pdb=" CG PRO f 5 " ideal model delta sigma weight residual 1.492 1.604 -0.112 5.00e-02 4.00e+02 5.05e+00 bond pdb=" CB TRP d 152 " pdb=" CG TRP d 152 " ideal model delta sigma weight residual 1.498 1.435 0.063 3.10e-02 1.04e+03 4.15e+00 bond pdb=" CG1 ILE a 201 " pdb=" CD1 ILE a 201 " ideal model delta sigma weight residual 1.513 1.446 0.067 3.90e-02 6.57e+02 2.96e+00 bond pdb=" SD MET j 31 " pdb=" CE MET j 31 " ideal model delta sigma weight residual 1.791 1.753 0.038 2.50e-02 1.60e+03 2.32e+00 ... (remaining 20845 not shown) Histogram of bond angle deviations from ideal: 94.04 - 102.03: 40 102.03 - 110.02: 18953 110.02 - 118.01: 9722 118.01 - 126.00: 8957 126.00 - 133.99: 181 Bond angle restraints: 37853 Sorted by residual: angle pdb=" CA PRO f 5 " pdb=" N PRO f 5 " pdb=" CD PRO f 5 " ideal model delta sigma weight residual 112.00 105.89 6.11 1.40e+00 5.10e-01 1.90e+01 angle pdb=" C ALA b 133 " pdb=" N MET b 134 " pdb=" CA MET b 134 " ideal model delta sigma weight residual 121.14 113.91 7.23 1.75e+00 3.27e-01 1.71e+01 angle pdb=" N GLY h 26 " pdb=" CA GLY h 26 " pdb=" C GLY h 26 " ideal model delta sigma weight residual 113.27 108.08 5.19 1.33e+00 5.65e-01 1.52e+01 angle pdb=" CB MET b 134 " pdb=" CG MET b 134 " pdb=" SD MET b 134 " ideal model delta sigma weight residual 112.70 101.26 11.44 3.00e+00 1.11e-01 1.46e+01 angle pdb=" CA TYR h 35 " pdb=" CB TYR h 35 " pdb=" CG TYR h 35 " ideal model delta sigma weight residual 113.90 120.17 -6.27 1.80e+00 3.09e-01 1.21e+01 ... (remaining 37848 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 8608 17.91 - 35.83: 820 35.83 - 53.74: 256 53.74 - 71.66: 52 71.66 - 89.57: 15 Dihedral angle restraints: 9751 sinusoidal: 5311 harmonic: 4440 Sorted by residual: dihedral pdb=" CA PHE K 73 " pdb=" C PHE K 73 " pdb=" N ALA K 74 " pdb=" CA ALA K 74 " ideal model delta harmonic sigma weight residual 180.00 156.49 23.51 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA SER a 91 " pdb=" C SER a 91 " pdb=" N PHE a 92 " pdb=" CA PHE a 92 " ideal model delta harmonic sigma weight residual 180.00 157.24 22.76 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA GLY h 26 " pdb=" C GLY h 26 " pdb=" N GLY h 27 " pdb=" CA GLY h 27 " ideal model delta harmonic sigma weight residual 180.00 159.15 20.85 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 9748 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1430 0.064 - 0.129: 191 0.129 - 0.193: 7 0.193 - 0.257: 0 0.257 - 0.322: 1 Chirality restraints: 1629 Sorted by residual: chirality pdb=" CG LEU K 65 " pdb=" CB LEU K 65 " pdb=" CD1 LEU K 65 " pdb=" CD2 LEU K 65 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CB ILE a 106 " pdb=" CA ILE a 106 " pdb=" CG1 ILE a 106 " pdb=" CG2 ILE a 106 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.78e-01 chirality pdb=" CA MET K 60 " pdb=" N MET K 60 " pdb=" C MET K 60 " pdb=" CB MET K 60 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.43e-01 ... (remaining 1626 not shown) Planarity restraints: 2969 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN a 152 " -0.044 5.00e-02 4.00e+02 6.63e-02 7.03e+00 pdb=" N PRO a 153 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO a 153 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO a 153 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE L 63 " 0.030 2.00e-02 2.50e+03 1.52e-02 6.91e+00 pdb=" CG PHE L 63 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE L 63 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE L 63 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE L 63 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE L 63 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE L 63 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 PHE L 63 " -0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE L 63 " -0.003 2.00e-02 2.50e+03 pdb=" HE1 PHE L 63 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE L 63 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE L 63 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG a 159 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.88e+00 pdb=" C ARG a 159 " 0.038 2.00e-02 2.50e+03 pdb=" O ARG a 159 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU a 160 " -0.013 2.00e-02 2.50e+03 ... (remaining 2966 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 779 2.12 - 2.74: 39191 2.74 - 3.36: 61357 3.36 - 3.98: 71044 3.98 - 4.60: 112008 Nonbonded interactions: 284379 Sorted by model distance: nonbonded pdb=" O ALA d 27 " pdb=" H LYS d 31 " model vdw 1.499 1.850 nonbonded pdb=" OE2 GLU S 168 " pdb=" H THR C 28 " model vdw 1.535 1.850 nonbonded pdb=" OE1 GLU h 34 " pdb=" H GLU h 34 " model vdw 1.542 1.850 nonbonded pdb=" OE1 GLU d 46 " pdb=" H GLU d 46 " model vdw 1.550 1.850 nonbonded pdb="HH21 ARG S 165 " pdb=" O GLY S 167 " model vdw 1.565 1.850 ... (remaining 284374 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 'K' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name HA or name HB1 or name HB2 or name HB3)) or resid 20 through 75)) selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.300 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: 0.290 Extract box with map and model: 27.340 Check model and map are aligned: 0.340 Set scattering table: 0.160 Process input model: 63.500 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: 0.010 Load rotamer database and sin/cos tables:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 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 0.112 10404 Z= 0.344 Angle : 0.741 11.445 14063 Z= 0.426 Chirality : 0.042 0.322 1629 Planarity : 0.006 0.066 1740 Dihedral : 15.190 89.574 3838 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 23.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.60 % Favored : 89.40 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.22), residues: 1264 helix: -0.68 (0.16), residues: 883 sheet: -2.13 (0.76), residues: 38 loop : -2.45 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP a 109 HIS 0.008 0.002 HIS S 112 PHE 0.043 0.002 PHE L 63 TYR 0.024 0.002 TYR h 18 ARG 0.011 0.001 ARG d 122 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue TYR 21 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue MET 27 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue TYR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ILE 40 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 1.710 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: 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 111 ILE cc_start: 0.8632 (mt) cc_final: 0.8412 (mm) REVERT: e 29 TYR cc_start: 0.8418 (t80) cc_final: 0.8182 (t80) REVERT: g 29 PHE cc_start: 0.7162 (m-10) cc_final: 0.6899 (m-80) REVERT: K 70 LEU cc_start: 0.8821 (mp) cc_final: 0.8608 (mm) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.4340 time to fit residues: 136.7694 Evaluate side-chains 182 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 145 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10404 Z= 0.265 Angle : 0.635 6.455 14063 Z= 0.348 Chirality : 0.039 0.148 1629 Planarity : 0.006 0.066 1740 Dihedral : 5.669 48.202 1392 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 19.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 0.83 % Allowed : 9.47 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.23), residues: 1264 helix: -0.45 (0.16), residues: 886 sheet: -2.04 (0.77), residues: 36 loop : -2.23 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP d 33 HIS 0.003 0.001 HIS b 158 PHE 0.026 0.002 PHE L 63 TYR 0.026 0.002 TYR h 35 ARG 0.005 0.000 ARG e 14 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue TYR 21 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue MET 27 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue TYR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ILE 40 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Evaluate side-chains 199 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 190 time to evaluate : 1.820 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: 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 111 ILE cc_start: 0.8481 (mt) cc_final: 0.8279 (mm) REVERT: e 29 TYR cc_start: 0.8416 (t80) cc_final: 0.8193 (t80) REVERT: g 29 PHE cc_start: 0.7150 (m-10) cc_final: 0.6896 (m-80) REVERT: K 70 LEU cc_start: 0.8819 (mp) cc_final: 0.8584 (mm) outliers start: 9 outliers final: 8 residues processed: 193 average time/residue: 0.4047 time to fit residues: 115.1706 Evaluate side-chains 191 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 183 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 62 ASN Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain f residue 85 LYS Chi-restraints excluded: chain g residue 73 LEU Chi-restraints excluded: chain R residue 47 PHE Chi-restraints excluded: chain R residue 54 PHE Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain b residue 57 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 109 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 101 ASN ** a 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 136 ASN ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10404 Z= 0.195 Angle : 0.584 6.834 14063 Z= 0.313 Chirality : 0.038 0.139 1629 Planarity : 0.005 0.060 1740 Dihedral : 5.304 47.927 1392 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 1.38 % Allowed : 11.03 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.23), residues: 1264 helix: -0.06 (0.17), residues: 887 sheet: -2.01 (0.78), residues: 36 loop : -1.93 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP a 109 HIS 0.002 0.001 HIS b 158 PHE 0.027 0.001 PHE L 63 TYR 0.020 0.001 TYR h 35 ARG 0.004 0.000 ARG e 14 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue TYR 21 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue MET 27 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue TYR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ILE 40 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Evaluate side-chains 216 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 201 time to evaluate : 1.730 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 29 PHE cc_start: 0.7156 (m-10) cc_final: 0.6898 (m-80) REVERT: K 70 LEU cc_start: 0.8795 (mp) cc_final: 0.8545 (mm) outliers start: 15 outliers final: 10 residues processed: 207 average time/residue: 0.3947 time to fit residues: 121.1427 Evaluate side-chains 201 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 191 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain g residue 73 LEU Chi-restraints excluded: chain R residue 47 PHE Chi-restraints excluded: chain R residue 54 PHE Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain b residue 57 THR Chi-restraints excluded: chain b residue 153 ASN Chi-restraints excluded: chain b residue 193 THR Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 159 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10404 Z= 0.224 Angle : 0.599 7.131 14063 Z= 0.320 Chirality : 0.038 0.160 1629 Planarity : 0.005 0.061 1740 Dihedral : 5.248 48.425 1392 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 1.56 % Allowed : 12.04 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.23), residues: 1264 helix: 0.09 (0.17), residues: 885 sheet: -1.92 (0.78), residues: 36 loop : -1.87 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP a 109 HIS 0.003 0.001 HIS b 158 PHE 0.025 0.001 PHE L 63 TYR 0.018 0.002 TYR h 35 ARG 0.004 0.000 ARG e 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue TYR 21 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue MET 27 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue TYR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ILE 40 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Evaluate side-chains 205 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 188 time to evaluate : 1.411 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 29 PHE cc_start: 0.7161 (m-10) cc_final: 0.6907 (m-80) REVERT: R 58 GLU cc_start: 0.7833 (tt0) cc_final: 0.7596 (tt0) REVERT: C 62 MET cc_start: 0.7780 (ppp) cc_final: 0.7542 (ppp) outliers start: 17 outliers final: 15 residues processed: 194 average time/residue: 0.3776 time to fit residues: 109.5198 Evaluate side-chains 199 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 184 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 98 LEU Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain g residue 73 LEU Chi-restraints excluded: chain R residue 47 PHE Chi-restraints excluded: chain R residue 54 PHE Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain b residue 57 THR Chi-restraints excluded: chain b residue 153 ASN Chi-restraints excluded: chain b residue 193 THR Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 159 MET Chi-restraints excluded: chain S residue 164 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 39 optimal weight: 0.0170 overall best weight: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 101 ASN ** a 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10404 Z= 0.207 Angle : 0.584 6.745 14063 Z= 0.311 Chirality : 0.038 0.138 1629 Planarity : 0.005 0.059 1740 Dihedral : 5.127 48.431 1392 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 2.11 % Allowed : 12.50 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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 (0.24), residues: 1264 helix: 0.23 (0.17), residues: 886 sheet: -1.90 (0.79), residues: 36 loop : -1.71 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP d 33 HIS 0.002 0.001 HIS b 172 PHE 0.018 0.001 PHE L 63 TYR 0.018 0.001 TYR e 29 ARG 0.004 0.000 ARG e 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue TYR 21 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue MET 27 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue TYR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ILE 40 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Evaluate side-chains 206 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 183 time to evaluate : 1.733 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 29 PHE cc_start: 0.7169 (m-10) cc_final: 0.6932 (m-80) REVERT: R 58 GLU cc_start: 0.7730 (tt0) cc_final: 0.7506 (tt0) REVERT: C 62 MET cc_start: 0.7774 (ppp) cc_final: 0.7527 (ppp) outliers start: 23 outliers final: 15 residues processed: 193 average time/residue: 0.3823 time to fit residues: 109.6441 Evaluate side-chains 199 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 184 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 98 LEU Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain g residue 73 LEU Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 47 PHE Chi-restraints excluded: chain R residue 54 PHE Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain b residue 57 THR Chi-restraints excluded: chain b residue 153 ASN Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 159 MET Chi-restraints excluded: chain S residue 164 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 28 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 0.0010 chunk 9 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 101 ASN ** a 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10404 Z= 0.166 Angle : 0.564 6.753 14063 Z= 0.295 Chirality : 0.038 0.163 1629 Planarity : 0.005 0.058 1740 Dihedral : 4.911 47.338 1392 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.38 % Allowed : 13.79 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -0.23 (0.24), residues: 1264 helix: 0.53 (0.18), residues: 882 sheet: -1.85 (0.79), residues: 36 loop : -1.56 (0.36), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP a 48 HIS 0.002 0.000 HIS b 172 PHE 0.014 0.001 PHE L 63 TYR 0.019 0.001 TYR j 21 ARG 0.003 0.000 ARG e 14 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue TYR 21 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue MET 27 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue TYR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ILE 40 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 197 time to evaluate : 1.636 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 29 PHE cc_start: 0.7108 (m-10) cc_final: 0.6864 (m-80) REVERT: g 87 TYR cc_start: 0.8639 (m-80) cc_final: 0.8164 (m-80) REVERT: j 31 MET cc_start: 0.7461 (mmm) cc_final: 0.6822 (mmm) REVERT: L 60 MET cc_start: 0.6510 (mmm) cc_final: 0.6235 (mmt) REVERT: b 102 LYS cc_start: 0.8541 (mmmm) cc_final: 0.8254 (ttpp) REVERT: C 62 MET cc_start: 0.7812 (ppp) cc_final: 0.7579 (ppp) outliers start: 15 outliers final: 13 residues processed: 202 average time/residue: 0.4034 time to fit residues: 119.9549 Evaluate side-chains 196 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 183 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 98 LEU Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 47 PHE Chi-restraints excluded: chain R residue 54 PHE Chi-restraints excluded: chain R residue 64 CYS Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain b residue 153 ASN Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 159 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 65 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 101 ASN ** a 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10404 Z= 0.179 Angle : 0.567 8.626 14063 Z= 0.297 Chirality : 0.037 0.133 1629 Planarity : 0.005 0.057 1740 Dihedral : 4.834 47.130 1392 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.47 % Allowed : 15.07 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -0.10 (0.24), residues: 1264 helix: 0.58 (0.17), residues: 890 sheet: -1.90 (0.78), residues: 36 loop : -1.39 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 109 HIS 0.002 0.001 HIS b 172 PHE 0.015 0.001 PHE L 63 TYR 0.019 0.001 TYR e 29 ARG 0.004 0.000 ARG e 14 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue TYR 21 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue MET 27 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue TYR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ILE 40 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Evaluate side-chains 204 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 188 time to evaluate : 1.589 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 29 PHE cc_start: 0.7108 (m-10) cc_final: 0.6867 (m-80) REVERT: g 87 TYR cc_start: 0.8643 (m-80) cc_final: 0.8186 (m-80) REVERT: j 31 MET cc_start: 0.7410 (mmm) cc_final: 0.6929 (mmp) REVERT: L 60 MET cc_start: 0.6838 (mmm) cc_final: 0.6513 (mmt) REVERT: C 62 MET cc_start: 0.7803 (ppp) cc_final: 0.7575 (ppp) outliers start: 16 outliers final: 15 residues processed: 194 average time/residue: 0.3879 time to fit residues: 112.1894 Evaluate side-chains 198 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 183 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 98 LEU Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain g residue 73 LEU Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 47 PHE Chi-restraints excluded: chain R residue 54 PHE Chi-restraints excluded: chain R residue 64 CYS Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain b residue 153 ASN Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 159 MET Chi-restraints excluded: chain S residue 164 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 57 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 106 optimal weight: 0.0470 chunk 111 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 overall best weight: 0.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 101 ASN ** a 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10404 Z= 0.174 Angle : 0.573 8.129 14063 Z= 0.299 Chirality : 0.038 0.171 1629 Planarity : 0.005 0.057 1740 Dihedral : 4.735 46.464 1392 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.65 % Allowed : 15.53 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.20 (0.24), residues: 1264 helix: 0.78 (0.18), residues: 875 sheet: -1.93 (0.79), residues: 36 loop : -1.09 (0.36), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP a 109 HIS 0.002 0.001 HIS b 172 PHE 0.015 0.001 PHE L 54 TYR 0.019 0.001 TYR e 29 ARG 0.003 0.000 ARG e 14 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue TYR 21 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue MET 27 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue TYR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ILE 40 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Evaluate side-chains 207 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 189 time to evaluate : 1.629 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 29 PHE cc_start: 0.7101 (m-10) cc_final: 0.6865 (m-80) REVERT: g 87 TYR cc_start: 0.8611 (m-80) cc_final: 0.8131 (m-80) REVERT: j 31 MET cc_start: 0.7419 (mmm) cc_final: 0.6804 (mmm) REVERT: b 102 LYS cc_start: 0.8524 (mmmm) cc_final: 0.8244 (ttpp) REVERT: C 62 MET cc_start: 0.7827 (ppp) cc_final: 0.7585 (ppp) outliers start: 18 outliers final: 15 residues processed: 196 average time/residue: 0.4353 time to fit residues: 127.4273 Evaluate side-chains 200 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 185 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 98 LEU Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 47 PHE Chi-restraints excluded: chain R residue 54 PHE Chi-restraints excluded: chain R residue 64 CYS Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain b residue 153 ASN Chi-restraints excluded: chain b residue 193 THR Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 159 MET Chi-restraints excluded: chain S residue 164 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 0.5980 chunk 65 optimal weight: 9.9990 chunk 47 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 101 ASN ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10404 Z= 0.172 Angle : 0.568 7.946 14063 Z= 0.295 Chirality : 0.037 0.163 1629 Planarity : 0.005 0.057 1740 Dihedral : 4.666 45.821 1392 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.10 % Allowed : 15.90 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.28 (0.24), residues: 1264 helix: 0.84 (0.18), residues: 879 sheet: -1.88 (0.79), residues: 36 loop : -1.10 (0.36), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 109 HIS 0.002 0.000 HIS b 172 PHE 0.012 0.001 PHE L 63 TYR 0.016 0.001 TYR b 157 ARG 0.003 0.000 ARG e 14 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue TYR 21 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue MET 27 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue TYR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ILE 40 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Evaluate side-chains 201 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 189 time to evaluate : 1.822 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 29 PHE cc_start: 0.7095 (m-10) cc_final: 0.6865 (m-80) REVERT: g 87 TYR cc_start: 0.8587 (m-80) cc_final: 0.8120 (m-80) REVERT: j 31 MET cc_start: 0.7353 (mmm) cc_final: 0.6624 (mmm) REVERT: L 60 MET cc_start: 0.6679 (mmm) cc_final: 0.6299 (mmt) REVERT: C 62 MET cc_start: 0.7790 (ppp) cc_final: 0.7554 (ppp) outliers start: 12 outliers final: 11 residues processed: 192 average time/residue: 0.4259 time to fit residues: 121.7162 Evaluate side-chains 192 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 181 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 98 LEU Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 47 PHE Chi-restraints excluded: chain R residue 54 PHE Chi-restraints excluded: chain R residue 64 CYS Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 159 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 120 optimal weight: 0.4980 chunk 110 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 29 optimal weight: 0.2980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 101 ASN ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10404 Z= 0.178 Angle : 0.567 6.844 14063 Z= 0.296 Chirality : 0.037 0.167 1629 Planarity : 0.005 0.057 1740 Dihedral : 4.638 45.502 1392 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.10 % Allowed : 16.08 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.31 (0.24), residues: 1264 helix: 0.86 (0.18), residues: 879 sheet: -1.90 (0.80), residues: 36 loop : -1.10 (0.36), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP a 109 HIS 0.002 0.001 HIS b 158 PHE 0.014 0.001 PHE S 141 TYR 0.017 0.001 TYR b 157 ARG 0.004 0.000 ARG e 14 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue TYR 21 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue MET 27 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue TYR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ILE 40 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 181 time to evaluate : 1.623 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 29 PHE cc_start: 0.7095 (m-10) cc_final: 0.6866 (m-80) REVERT: g 87 TYR cc_start: 0.8576 (m-80) cc_final: 0.8126 (m-80) REVERT: j 31 MET cc_start: 0.7346 (mmm) cc_final: 0.6523 (mmm) REVERT: C 62 MET cc_start: 0.7787 (ppp) cc_final: 0.7546 (ppp) outliers start: 12 outliers final: 11 residues processed: 185 average time/residue: 0.4131 time to fit residues: 113.1854 Evaluate side-chains 190 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 179 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 98 LEU Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 47 PHE Chi-restraints excluded: chain R residue 54 PHE Chi-restraints excluded: chain R residue 64 CYS Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 159 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 101 ASN ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.087845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.080317 restraints weight = 175508.529| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 3.40 r_work: 0.3780 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10404 Z= 0.178 Angle : 0.562 6.687 14063 Z= 0.293 Chirality : 0.037 0.173 1629 Planarity : 0.005 0.057 1740 Dihedral : 4.608 45.057 1392 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.10 % Allowed : 16.27 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.36 (0.24), residues: 1264 helix: 0.90 (0.18), residues: 879 sheet: -1.95 (0.78), residues: 36 loop : -1.08 (0.36), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP a 109 HIS 0.002 0.001 HIS b 172 PHE 0.012 0.001 PHE L 63 TYR 0.017 0.001 TYR b 157 ARG 0.004 0.000 ARG e 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4706.13 seconds wall clock time: 84 minutes 27.50 seconds (5067.50 seconds total)