Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 17:09:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zit_11229/04_2023/6zit_11229_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zit_11229/04_2023/6zit_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_11229/04_2023/6zit_11229.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zit_11229/04_2023/6zit_11229.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zit_11229/04_2023/6zit_11229_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zit_11229/04_2023/6zit_11229_trim_updated.pdb" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 9.03, 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: 17.54 Conformation dependent library (CDL) restraints added in 1.8 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: 1.33 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: 7.30 Time building geometry restraints manager: 17.83 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: 7405 17.91 - 35.83: 745 35.83 - 53.74: 128 53.74 - 71.66: 29 71.66 - 89.57: 15 Dihedral angle restraints: 8322 sinusoidal: 3882 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 8319 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: 10.830 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: 27.860 Check model and map are aligned: 0.350 Set scattering table: 0.180 Process input model: 64.450 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.390 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 1.757 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 outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.4508 time to fit residues: 141.1479 Evaluate side-chains 182 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.588 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2885 ------------------------------------------------------------------------------- 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: 1.9990 chunk 36 optimal weight: 0.0170 chunk 57 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.1824 ------------------------------------------------------------------------------- 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** ** b 115 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: 0.7424 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 10404 Z= 0.215 Angle : 0.618 5.974 14063 Z= 0.334 Chirality : 0.038 0.140 1629 Planarity : 0.005 0.066 1740 Dihedral : 5.558 47.617 1392 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer Outliers : 1.01 % 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: -1.35 (0.23), residues: 1264 helix: -0.29 (0.17), residues: 886 sheet: -2.01 (0.77), residues: 36 loop : -2.11 (0.34), residues: 342 *********************** 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 210 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 199 time to evaluate : 1.671 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 outliers start: 11 outliers final: 9 residues processed: 204 average time/residue: 0.4163 time to fit residues: 124.4560 Evaluate side-chains 192 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 183 time to evaluate : 1.712 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2859 time to fit residues: 6.3366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 118 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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: 0.7412 moved from start: 0.1407 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= 0.206 Angle : 0.595 6.464 14063 Z= 0.318 Chirality : 0.038 0.155 1629 Planarity : 0.005 0.062 1740 Dihedral : 5.300 47.824 1392 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer Outliers : 0.37 % 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: -0.93 (0.23), residues: 1264 helix: 0.01 (0.17), residues: 886 sheet: -1.88 (0.78), residues: 36 loop : -1.89 (0.35), residues: 342 *********************** 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 200 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 196 time to evaluate : 2.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 outliers start: 4 outliers final: 3 residues processed: 198 average time/residue: 0.3911 time to fit residues: 115.8699 Evaluate side-chains 189 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 186 time to evaluate : 1.639 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2139 time to fit residues: 3.2807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 57 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 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: 0.7412 moved from start: 0.1616 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= 0.208 Angle : 0.590 7.299 14063 Z= 0.314 Chirality : 0.038 0.139 1629 Planarity : 0.005 0.063 1740 Dihedral : 5.193 47.948 1392 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer Outliers : 1.38 % 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: -0.74 (0.23), residues: 1264 helix: 0.13 (0.17), residues: 891 sheet: -1.86 (0.79), residues: 36 loop : -1.78 (0.35), residues: 337 *********************** 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 204 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 189 time to evaluate : 1.943 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 outliers start: 15 outliers final: 9 residues processed: 195 average time/residue: 0.4067 time to fit residues: 118.0545 Evaluate side-chains 193 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 184 time to evaluate : 1.793 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2406 time to fit residues: 6.0675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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** 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: 0.7420 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 10404 Z= 0.218 Angle : 0.591 6.724 14063 Z= 0.314 Chirality : 0.038 0.139 1629 Planarity : 0.005 0.063 1740 Dihedral : 5.127 48.188 1392 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer Outliers : 0.74 % 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: -0.53 (0.24), residues: 1264 helix: 0.27 (0.17), residues: 884 sheet: -1.88 (0.79), residues: 36 loop : -1.61 (0.35), residues: 344 *********************** 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 189 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 181 time to evaluate : 1.634 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 outliers start: 8 outliers final: 5 residues processed: 184 average time/residue: 0.3954 time to fit residues: 108.3299 Evaluate side-chains 183 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 178 time to evaluate : 1.720 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2185 time to fit residues: 4.0204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 0.0770 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 overall best weight: 1.2146 ------------------------------------------------------------------------------- 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: 0.7406 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 10404 Z= 0.200 Angle : 0.584 8.386 14063 Z= 0.307 Chirality : 0.038 0.136 1629 Planarity : 0.005 0.064 1740 Dihedral : 5.005 47.911 1392 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer Outliers : 1.01 % 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: -0.35 (0.24), residues: 1264 helix: 0.40 (0.17), residues: 880 sheet: -1.83 (0.79), residues: 36 loop : -1.51 (0.35), residues: 348 *********************** 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 198 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 187 time to evaluate : 1.695 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 outliers start: 11 outliers final: 8 residues processed: 190 average time/residue: 0.3989 time to fit residues: 112.4578 Evaluate side-chains 184 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 176 time to evaluate : 1.565 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2201 time to fit residues: 5.2322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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: 0.7402 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 10404 Z= 0.195 Angle : 0.584 8.237 14063 Z= 0.305 Chirality : 0.037 0.145 1629 Planarity : 0.004 0.062 1740 Dihedral : 4.941 47.761 1392 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer Outliers : 0.37 % 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: 0.48 (0.17), residues: 883 sheet: -1.89 (0.79), residues: 36 loop : -1.44 (0.36), residues: 345 *********************** 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 188 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 184 time to evaluate : 1.923 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 outliers start: 4 outliers final: 3 residues processed: 184 average time/residue: 0.3981 time to fit residues: 109.2349 Evaluate side-chains 178 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 175 time to evaluate : 1.683 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2420 time to fit residues: 3.3228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 chunk 91 optimal weight: 3.9990 chunk 106 optimal weight: 0.0370 chunk 111 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- 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: 0.7375 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 10404 Z= 0.173 Angle : 0.573 9.114 14063 Z= 0.295 Chirality : 0.037 0.134 1629 Planarity : 0.004 0.062 1740 Dihedral : 4.786 46.669 1392 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer Outliers : 0.55 % 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: 0.03 (0.24), residues: 1264 helix: 0.66 (0.18), residues: 883 sheet: -1.78 (0.80), residues: 36 loop : -1.27 (0.36), residues: 345 *********************** 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 191 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 185 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 outliers start: 6 outliers final: 5 residues processed: 186 average time/residue: 0.4196 time to fit residues: 114.3122 Evaluate side-chains 184 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 179 time to evaluate : 1.656 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2396 time to fit residues: 4.1542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 71 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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** ** 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: 0.7390 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 10404 Z= 0.191 Angle : 0.575 7.891 14063 Z= 0.300 Chirality : 0.037 0.154 1629 Planarity : 0.004 0.063 1740 Dihedral : 4.741 46.661 1392 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer Outliers : 0.37 % 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: 0.11 (0.24), residues: 1264 helix: 0.74 (0.18), residues: 877 sheet: -1.79 (0.80), residues: 36 loop : -1.29 (0.36), residues: 351 *********************** 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 185 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 181 time to evaluate : 1.782 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 outliers start: 4 outliers final: 3 residues processed: 182 average time/residue: 0.4176 time to fit residues: 113.3621 Evaluate side-chains 178 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 175 time to evaluate : 1.842 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2408 time to fit residues: 3.2869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 0.0470 chunk 79 optimal weight: 0.0270 chunk 120 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.0140 ------------------------------------------------------------------------------- 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: 0.7384 moved from start: 0.2561 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= 0.182 Angle : 0.575 8.111 14063 Z= 0.298 Chirality : 0.037 0.168 1629 Planarity : 0.004 0.062 1740 Dihedral : 4.695 46.104 1392 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer Outliers : 0.18 % 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: 0.21 (0.24), residues: 1264 helix: 0.80 (0.18), residues: 878 sheet: -1.75 (0.81), residues: 36 loop : -1.19 (0.36), residues: 350 ********************** 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 186 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 184 time to evaluate : 1.814 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 outliers start: 2 outliers final: 2 residues processed: 184 average time/residue: 0.4304 time to fit residues: 116.1906 Evaluate side-chains 178 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 176 time to evaluate : 1.696 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2734 time to fit residues: 2.9562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 40 optimal weight: 0.1980 chunk 98 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 5 optimal weight: 0.0770 chunk 69 optimal weight: 0.8980 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 223 HIS ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.088254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.080758 restraints weight = 173694.370| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 3.35 r_work: 0.3790 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 10404 Z= 0.168 Angle : 0.576 7.621 14063 Z= 0.297 Chirality : 0.037 0.158 1629 Planarity : 0.004 0.062 1740 Dihedral : 4.605 44.927 1392 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer Outliers : 0.46 % 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: 0.40 (0.25), residues: 1264 helix: 0.92 (0.18), residues: 879 sheet: -1.76 (0.81), residues: 36 loop : -1.03 (0.36), residues: 349 =============================================================================== Job complete usr+sys time: 4600.93 seconds wall clock time: 83 minutes 21.01 seconds (5001.01 seconds total)