Starting phenix.real_space_refine on Tue Sep 24 16:11:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5a_0670/09_2024/6j5a_0670.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5a_0670/09_2024/6j5a_0670.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5a_0670/09_2024/6j5a_0670.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5a_0670/09_2024/6j5a_0670.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5a_0670/09_2024/6j5a_0670.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5a_0670/09_2024/6j5a_0670.cif" } resolution = 4.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 5542 2.51 5 N 1423 2.21 5 O 1530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8544 Number of models: 1 Model: "" Number of chains: 18 Chain: "b" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 440 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 5, 'TRANS': 76} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 272 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 5, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 99 Chain: "d" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 1, 'TRANS': 22} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 47 Chain: "e" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 315 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'TRANS': 62} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'UNK:plan-1': 63} Unresolved non-hydrogen planarities: 63 Chain: "f" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 530 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 3, 'TRANS': 83} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 112 Chain: "g" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 420 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'TRANS': 83} Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 252 Unresolved non-hydrogen dihedrals: 84 Planarities with less than four sites: {'UNK:plan-1': 84} Unresolved non-hydrogen planarities: 84 Chain: "i" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 306 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 41} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "k" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 145 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'TRANS': 28} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'UNK:plan-1': 29} Unresolved non-hydrogen planarities: 29 Chain: "8" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 251 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "a" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1706 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 210} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "K" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "L" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "M" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "N" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 510 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 70} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "O" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "P" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "Q" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "R" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "u" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 210 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'TRANS': 41} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'UNK:plan-1': 42} Unresolved non-hydrogen planarities: 42 Time building chain proxies: 5.83, per 1000 atoms: 0.68 Number of scatterers: 8544 At special positions: 0 Unit cell: (111.78, 109.02, 113.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 49 16.00 O 1530 8.00 N 1423 7.00 C 5542 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.40 Conformation dependent library (CDL) restraints added in 1.0 seconds 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2326 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 0 sheets defined 89.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'b' and resid 3 through 31 Proline residue: b 18 - end of helix Proline residue: b 27 - end of helix removed outlier: 3.504A pdb=" N VAL b 31 " --> pdb=" O PRO b 27 " (cutoff:3.500A) Processing helix chain 'b' and resid 37 through 42 removed outlier: 3.917A pdb=" N LEU b 41 " --> pdb=" O LEU b 37 " (cutoff:3.500A) Processing helix chain 'b' and resid 43 through 48 Processing helix chain 'b' and resid 49 through 51 No H-bonds generated for 'chain 'b' and resid 49 through 51' Processing helix chain 'b' and resid 61 through 83 removed outlier: 4.190A pdb=" N LEU b 67 " --> pdb=" O THR b 63 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL b 68 " --> pdb=" O ILE b 64 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR b 69 " --> pdb=" O GLY b 65 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE b 70 " --> pdb=" O VAL b 66 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL b 71 " --> pdb=" O LEU b 67 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS b 72 " --> pdb=" O VAL b 68 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS b 73 " --> pdb=" O TYR b 69 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY b 75 " --> pdb=" O VAL b 71 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA b 76 " --> pdb=" O LYS b 72 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLY b 79 " --> pdb=" O GLY b 75 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA b 80 " --> pdb=" O ALA b 76 " (cutoff:3.500A) Processing helix chain 'd' and resid 133 through 137 removed outlier: 3.864A pdb=" N GLU d 137 " --> pdb=" O ASP d 134 " (cutoff:3.500A) Processing helix chain 'e' and resid 5 through 63 removed outlier: 3.501A pdb=" N UNK e 42 " --> pdb=" O UNK e 38 " (cutoff:3.500A) Processing helix chain 'f' and resid 2 through 15 removed outlier: 3.502A pdb=" N LYS f 7 " --> pdb=" O VAL f 3 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP f 8 " --> pdb=" O VAL f 4 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG f 9 " --> pdb=" O PRO f 5 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU f 11 " --> pdb=" O LYS f 7 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL f 14 " --> pdb=" O ARG f 10 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS f 15 " --> pdb=" O LEU f 11 " (cutoff:3.500A) Processing helix chain 'f' and resid 27 through 35 removed outlier: 3.749A pdb=" N GLY f 32 " --> pdb=" O PHE f 28 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE f 33 " --> pdb=" O THR f 29 " (cutoff:3.500A) Processing helix chain 'f' and resid 36 through 41 Processing helix chain 'f' and resid 42 through 44 No H-bonds generated for 'chain 'f' and resid 42 through 44' Processing helix chain 'f' and resid 55 through 60 removed outlier: 3.617A pdb=" N LEU f 59 " --> pdb=" O SER f 55 " (cutoff:3.500A) Processing helix chain 'f' and resid 61 through 75 removed outlier: 3.526A pdb=" N VAL f 67 " --> pdb=" O LEU f 63 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL f 68 " --> pdb=" O ALA f 64 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N CYS f 72 " --> pdb=" O VAL f 68 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG f 73 " --> pdb=" O PHE f 69 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER f 74 " --> pdb=" O ASN f 70 " (cutoff:3.500A) Processing helix chain 'g' and resid 2 through 32 removed outlier: 3.669A pdb=" N UNK g 7 " --> pdb=" O UNK g 3 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N UNK g 8 " --> pdb=" O UNK g 4 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N UNK g 18 " --> pdb=" O UNK g 14 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N UNK g 21 " --> pdb=" O UNK g 17 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N UNK g 25 " --> pdb=" O UNK g 21 " (cutoff:3.500A) Processing helix chain 'g' and resid 60 through 65 Processing helix chain 'g' and resid 65 through 84 removed outlier: 3.564A pdb=" N UNK g 74 " --> pdb=" O UNK g 70 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N UNK g 77 " --> pdb=" O UNK g 73 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N UNK g 78 " --> pdb=" O UNK g 74 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N UNK g 79 " --> pdb=" O UNK g 75 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N UNK g 83 " --> pdb=" O UNK g 79 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N UNK g 84 " --> pdb=" O UNK g 80 " (cutoff:3.500A) Processing helix chain 'i' and resid 14 through 26 removed outlier: 3.975A pdb=" N ASN i 19 " --> pdb=" O LYS i 15 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER i 20 " --> pdb=" O LYS i 16 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LEU i 23 " --> pdb=" O ASN i 19 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N THR i 24 " --> pdb=" O SER i 20 " (cutoff:3.500A) Processing helix chain 'i' and resid 27 through 48 removed outlier: 4.493A pdb=" N LEU i 31 " --> pdb=" O MET i 27 " (cutoff:3.500A) Processing helix chain 'k' and resid 12 through 29 removed outlier: 3.818A pdb=" N UNK k 16 " --> pdb=" O UNK k 12 " (cutoff:3.500A) Processing helix chain '8' and resid 12 through 16 removed outlier: 3.667A pdb=" N SER 8 15 " --> pdb=" O THR 8 12 " (cutoff:3.500A) Processing helix chain '8' and resid 19 through 28 removed outlier: 3.706A pdb=" N LEU 8 23 " --> pdb=" O THR 8 19 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLN 8 25 " --> pdb=" O PHE 8 21 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU 8 26 " --> pdb=" O ILE 8 22 " (cutoff:3.500A) Processing helix chain 'a' and resid 19 through 24 removed outlier: 4.165A pdb=" N ILE a 23 " --> pdb=" O ILE a 19 " (cutoff:3.500A) Processing helix chain 'a' and resid 25 through 29 Processing helix chain 'a' and resid 43 through 54 removed outlier: 3.796A pdb=" N LEU a 49 " --> pdb=" O ILE a 45 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN a 51 " --> pdb=" O GLN a 47 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR a 53 " --> pdb=" O LEU a 49 " (cutoff:3.500A) Processing helix chain 'a' and resid 68 through 73 removed outlier: 3.737A pdb=" N LEU a 72 " --> pdb=" O TRP a 68 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET a 73 " --> pdb=" O SER a 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 68 through 73' Processing helix chain 'a' and resid 73 through 82 removed outlier: 3.814A pdb=" N MET a 77 " --> pdb=" O MET a 73 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE a 79 " --> pdb=" O LEU a 75 " (cutoff:3.500A) Processing helix chain 'a' and resid 84 through 88 removed outlier: 3.820A pdb=" N LEU a 87 " --> pdb=" O ILE a 84 " (cutoff:3.500A) Processing helix chain 'a' and resid 93 through 96 Processing helix chain 'a' and resid 97 through 102 removed outlier: 4.551A pdb=" N ASN a 101 " --> pdb=" O GLN a 97 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU a 102 " --> pdb=" O LEU a 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 97 through 102' Processing helix chain 'a' and resid 105 through 117 removed outlier: 4.139A pdb=" N ALA a 111 " --> pdb=" O PRO a 107 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR a 112 " --> pdb=" O LEU a 108 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL a 113 " --> pdb=" O TRP a 109 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE a 114 " --> pdb=" O SER a 110 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR a 115 " --> pdb=" O ALA a 111 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY a 116 " --> pdb=" O THR a 112 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE a 117 " --> pdb=" O VAL a 113 " (cutoff:3.500A) Processing helix chain 'a' and resid 150 through 180 removed outlier: 4.580A pdb=" N VAL a 154 " --> pdb=" O PHE a 150 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG a 159 " --> pdb=" O ALA a 155 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU a 160 " --> pdb=" O LEU a 156 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASN a 163 " --> pdb=" O ARG a 159 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE a 164 " --> pdb=" O LEU a 160 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR a 165 " --> pdb=" O THR a 161 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA a 166 " --> pdb=" O ALA a 162 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS a 168 " --> pdb=" O ILE a 164 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU a 170 " --> pdb=" O ALA a 166 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR a 178 " --> pdb=" O ILE a 174 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU a 179 " --> pdb=" O GLY a 175 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 202 removed outlier: 4.207A pdb=" N PHE a 190 " --> pdb=" O THR a 186 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR a 200 " --> pdb=" O LEU a 196 " (cutoff:3.500A) Processing helix chain 'a' and resid 206 through 222 removed outlier: 3.834A pdb=" N GLN a 210 " --> pdb=" O VAL a 206 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA a 211 " --> pdb=" O ALA a 207 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TYR a 212 " --> pdb=" O LEU a 208 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N THR a 215 " --> pdb=" O ALA a 211 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU a 216 " --> pdb=" O TYR a 212 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER a 219 " --> pdb=" O THR a 215 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 15 removed outlier: 3.700A pdb=" N ILE K 9 " --> pdb=" O ALA K 5 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY K 12 " --> pdb=" O PHE K 8 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR K 15 " --> pdb=" O ALA K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 37 removed outlier: 3.958A pdb=" N GLY K 26 " --> pdb=" O GLY K 22 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR K 27 " --> pdb=" O ALA K 23 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL K 28 " --> pdb=" O GLY K 24 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE K 29 " --> pdb=" O ILE K 25 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET K 32 " --> pdb=" O VAL K 28 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE K 33 " --> pdb=" O PHE K 29 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE K 34 " --> pdb=" O GLY K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 73 removed outlier: 4.206A pdb=" N SER K 48 " --> pdb=" O GLN K 44 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU K 52 " --> pdb=" O SER K 48 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER K 57 " --> pdb=" O GLY K 53 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA K 59 " --> pdb=" O ALA K 55 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET K 60 " --> pdb=" O LEU K 56 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE K 63 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N CYS K 64 " --> pdb=" O MET K 60 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU K 65 " --> pdb=" O GLY K 61 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU K 72 " --> pdb=" O ALA K 68 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 15 removed outlier: 3.631A pdb=" N ILE L 9 " --> pdb=" O ALA L 5 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA L 11 " --> pdb=" O LYS L 7 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA L 13 " --> pdb=" O ILE L 9 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR L 15 " --> pdb=" O ALA L 11 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 24 Processing helix chain 'L' and resid 24 through 29 removed outlier: 4.195A pdb=" N VAL L 28 " --> pdb=" O GLY L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 35 removed outlier: 3.546A pdb=" N ILE L 34 " --> pdb=" O GLY L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 73 removed outlier: 4.140A pdb=" N SER L 48 " --> pdb=" O GLN L 44 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA L 50 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER L 57 " --> pdb=" O GLY L 53 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N MET L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY L 61 " --> pdb=" O SER L 57 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE L 63 " --> pdb=" O ALA L 59 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N CYS L 64 " --> pdb=" O MET L 60 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA L 68 " --> pdb=" O CYS L 64 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU L 72 " --> pdb=" O ALA L 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 14 removed outlier: 3.536A pdb=" N LYS M 7 " --> pdb=" O ASP M 3 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY M 12 " --> pdb=" O PHE M 8 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA M 14 " --> pdb=" O GLY M 10 " (cutoff:3.500A) Processing helix chain 'M' and resid 17 through 29 removed outlier: 4.418A pdb=" N SER M 21 " --> pdb=" O GLY M 17 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA M 23 " --> pdb=" O ALA M 19 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N GLY M 26 " --> pdb=" O GLY M 22 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL M 28 " --> pdb=" O GLY M 24 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE M 29 " --> pdb=" O ILE M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 32 through 39 removed outlier: 3.555A pdb=" N ARG M 38 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN M 39 " --> pdb=" O GLY M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 56 removed outlier: 4.172A pdb=" N SER M 48 " --> pdb=" O GLN M 44 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA M 50 " --> pdb=" O LEU M 46 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU M 52 " --> pdb=" O SER M 48 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY M 53 " --> pdb=" O TYR M 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 71 removed outlier: 3.989A pdb=" N LEU M 65 " --> pdb=" O GLY M 61 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL M 67 " --> pdb=" O PHE M 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 13 removed outlier: 3.513A pdb=" N PHE N 8 " --> pdb=" O THR N 4 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY N 10 " --> pdb=" O ALA N 6 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA N 11 " --> pdb=" O LYS N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 19 removed outlier: 3.631A pdb=" N GLY N 17 " --> pdb=" O ALA N 14 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 37 removed outlier: 3.569A pdb=" N ILE N 25 " --> pdb=" O SER N 21 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLY N 26 " --> pdb=" O GLY N 22 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL N 28 " --> pdb=" O GLY N 24 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET N 32 " --> pdb=" O VAL N 28 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE N 33 " --> pdb=" O PHE N 29 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE N 34 " --> pdb=" O GLY N 30 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY N 35 " --> pdb=" O SER N 31 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 63 removed outlier: 4.086A pdb=" N SER N 48 " --> pdb=" O GLN N 44 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA N 50 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE N 51 " --> pdb=" O PHE N 47 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU N 52 " --> pdb=" O SER N 48 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY N 53 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET N 60 " --> pdb=" O LEU N 56 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE N 63 " --> pdb=" O ALA N 59 " (cutoff:3.500A) Processing helix chain 'N' and resid 65 through 73 removed outlier: 3.511A pdb=" N PHE N 69 " --> pdb=" O LEU N 65 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU N 70 " --> pdb=" O MET N 66 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE N 71 " --> pdb=" O VAL N 67 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 12 removed outlier: 3.695A pdb=" N PHE O 8 " --> pdb=" O THR O 4 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE O 9 " --> pdb=" O ALA O 5 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY O 10 " --> pdb=" O ALA O 6 " (cutoff:3.500A) Processing helix chain 'O' and resid 21 through 31 removed outlier: 3.633A pdb=" N ILE O 25 " --> pdb=" O SER O 21 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR O 27 " --> pdb=" O ALA O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 32 through 37 Processing helix chain 'O' and resid 44 through 71 removed outlier: 3.966A pdb=" N SER O 48 " --> pdb=" O GLN O 44 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA O 50 " --> pdb=" O LEU O 46 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU O 56 " --> pdb=" O LEU O 52 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET O 60 " --> pdb=" O LEU O 56 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N CYS O 64 " --> pdb=" O MET O 60 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU O 65 " --> pdb=" O GLY O 61 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N MET O 66 " --> pdb=" O LEU O 62 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL O 67 " --> pdb=" O PHE O 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 14 removed outlier: 3.784A pdb=" N PHE P 8 " --> pdb=" O THR P 4 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ILE P 9 " --> pdb=" O ALA P 5 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA P 11 " --> pdb=" O LYS P 7 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY P 12 " --> pdb=" O PHE P 8 " (cutoff:3.500A) Processing helix chain 'P' and resid 17 through 26 removed outlier: 3.676A pdb=" N SER P 21 " --> pdb=" O GLY P 17 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY P 24 " --> pdb=" O GLY P 20 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 31 Processing helix chain 'P' and resid 32 through 37 Processing helix chain 'P' and resid 44 through 73 removed outlier: 4.411A pdb=" N SER P 48 " --> pdb=" O GLN P 44 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA P 50 " --> pdb=" O LEU P 46 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER P 57 " --> pdb=" O GLY P 53 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA P 59 " --> pdb=" O ALA P 55 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE P 63 " --> pdb=" O ALA P 59 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N CYS P 64 " --> pdb=" O MET P 60 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU P 65 " --> pdb=" O GLY P 61 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU P 70 " --> pdb=" O MET P 66 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE P 71 " --> pdb=" O VAL P 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 15 removed outlier: 3.643A pdb=" N PHE Q 8 " --> pdb=" O THR Q 4 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY Q 10 " --> pdb=" O ALA Q 6 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA Q 11 " --> pdb=" O LYS Q 7 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY Q 12 " --> pdb=" O PHE Q 8 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA Q 13 " --> pdb=" O ILE Q 9 " (cutoff:3.500A) Processing helix chain 'Q' and resid 18 through 24 Processing helix chain 'Q' and resid 27 through 37 removed outlier: 3.952A pdb=" N MET Q 32 " --> pdb=" O VAL Q 28 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE Q 33 " --> pdb=" O PHE Q 29 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE Q 34 " --> pdb=" O GLY Q 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 73 removed outlier: 3.829A pdb=" N SER Q 48 " --> pdb=" O GLN Q 44 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR Q 49 " --> pdb=" O GLN Q 45 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA Q 50 " --> pdb=" O LEU Q 46 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU Q 52 " --> pdb=" O SER Q 48 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE Q 54 " --> pdb=" O ALA Q 50 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS Q 64 " --> pdb=" O MET Q 60 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA Q 68 " --> pdb=" O CYS Q 64 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU Q 70 " --> pdb=" O MET Q 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 16 removed outlier: 3.812A pdb=" N PHE R 8 " --> pdb=" O THR R 4 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE R 9 " --> pdb=" O ALA R 5 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY R 10 " --> pdb=" O ALA R 6 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA R 14 " --> pdb=" O GLY R 10 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR R 15 " --> pdb=" O ALA R 11 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL R 16 " --> pdb=" O GLY R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 37 removed outlier: 4.294A pdb=" N SER R 21 " --> pdb=" O GLY R 17 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY R 22 " --> pdb=" O VAL R 18 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY R 26 " --> pdb=" O GLY R 22 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR R 27 " --> pdb=" O ALA R 23 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE R 29 " --> pdb=" O ILE R 25 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE R 33 " --> pdb=" O PHE R 29 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE R 34 " --> pdb=" O GLY R 30 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA R 37 " --> pdb=" O ILE R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 73 removed outlier: 3.664A pdb=" N SER R 48 " --> pdb=" O GLN R 44 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA R 50 " --> pdb=" O LEU R 46 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA R 55 " --> pdb=" O ILE R 51 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET R 60 " --> pdb=" O LEU R 56 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL R 67 " --> pdb=" O PHE R 63 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA R 68 " --> pdb=" O CYS R 64 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE R 69 " --> pdb=" O LEU R 65 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU R 72 " --> pdb=" O ALA R 68 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE R 73 " --> pdb=" O PHE R 69 " (cutoff:3.500A) Processing helix chain 'u' and resid 3 through 9 removed outlier: 3.632A pdb=" N UNK u 7 " --> pdb=" O UNK u 3 " (cutoff:3.500A) Processing helix chain 'u' and resid 16 through 35 removed outlier: 4.471A pdb=" N UNK u 20 " --> pdb=" O UNK u 16 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N UNK u 21 " --> pdb=" O UNK u 17 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N UNK u 29 " --> pdb=" O UNK u 25 " (cutoff:3.500A) 451 hydrogen bonds defined for protein. 1329 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: 2.01 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2698 1.34 - 1.46: 1859 1.46 - 1.58: 4020 1.58 - 1.70: 0 1.70 - 1.82: 88 Bond restraints: 8665 Sorted by residual: bond pdb=" C GLN a 152 " pdb=" N PRO a 153 " ideal model delta sigma weight residual 1.336 1.366 -0.030 1.20e-02 6.94e+03 6.41e+00 bond pdb=" CA THR b 32 " pdb=" C THR b 32 " ideal model delta sigma weight residual 1.523 1.553 -0.029 1.30e-02 5.92e+03 5.07e+00 bond pdb=" N ASN M 39 " pdb=" CA ASN M 39 " ideal model delta sigma weight residual 1.462 1.441 0.021 1.00e-02 1.00e+04 4.34e+00 bond pdb=" CB PHE a 214 " pdb=" CG PHE a 214 " ideal model delta sigma weight residual 1.502 1.454 0.048 2.30e-02 1.89e+03 4.31e+00 bond pdb=" N UNK g 38 " pdb=" CA UNK g 38 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.90e-02 2.77e+03 4.12e+00 ... (remaining 8660 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.04: 11454 3.04 - 6.07: 286 6.07 - 9.11: 37 9.11 - 12.15: 9 12.15 - 15.18: 1 Bond angle restraints: 11787 Sorted by residual: angle pdb=" C UNK g 37 " pdb=" N UNK g 38 " pdb=" CA UNK g 38 " ideal model delta sigma weight residual 121.70 136.88 -15.18 1.80e+00 3.09e-01 7.11e+01 angle pdb=" C SER 8 7 " pdb=" N THR 8 8 " pdb=" CA THR 8 8 " ideal model delta sigma weight residual 121.54 133.17 -11.63 1.91e+00 2.74e-01 3.71e+01 angle pdb=" N LEU a 136 " pdb=" CA LEU a 136 " pdb=" C LEU a 136 " ideal model delta sigma weight residual 113.01 119.93 -6.92 1.20e+00 6.94e-01 3.32e+01 angle pdb=" N ALA a 135 " pdb=" CA ALA a 135 " pdb=" C ALA a 135 " ideal model delta sigma weight residual 111.69 118.55 -6.86 1.23e+00 6.61e-01 3.11e+01 angle pdb=" N THR b 32 " pdb=" CA THR b 32 " pdb=" C THR b 32 " ideal model delta sigma weight residual 111.28 117.21 -5.93 1.09e+00 8.42e-01 2.96e+01 ... (remaining 11782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.31: 4272 14.31 - 28.62: 521 28.62 - 42.94: 154 42.94 - 57.25: 41 57.25 - 71.56: 6 Dihedral angle restraints: 4994 sinusoidal: 1377 harmonic: 3617 Sorted by residual: dihedral pdb=" CA THR 8 6 " pdb=" C THR 8 6 " pdb=" N SER 8 7 " pdb=" CA SER 8 7 " ideal model delta harmonic sigma weight residual -180.00 -131.76 -48.24 0 5.00e+00 4.00e-02 9.31e+01 dihedral pdb=" CA ILE f 23 " pdb=" C ILE f 23 " pdb=" N LEU f 24 " pdb=" CA LEU f 24 " ideal model delta harmonic sigma weight residual -180.00 -133.31 -46.69 0 5.00e+00 4.00e-02 8.72e+01 dihedral pdb=" CA THR 8 8 " pdb=" C THR 8 8 " pdb=" N TRP 8 9 " pdb=" CA TRP 8 9 " ideal model delta harmonic sigma weight residual 180.00 140.95 39.05 0 5.00e+00 4.00e-02 6.10e+01 ... (remaining 4991 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1035 0.047 - 0.095: 316 0.095 - 0.142: 88 0.142 - 0.190: 27 0.190 - 0.237: 12 Chirality restraints: 1478 Sorted by residual: chirality pdb=" CB THR 8 8 " pdb=" CA THR 8 8 " pdb=" OG1 THR 8 8 " pdb=" CG2 THR 8 8 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB VAL L 28 " pdb=" CA VAL L 28 " pdb=" CG1 VAL L 28 " pdb=" CG2 VAL L 28 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CB VAL K 18 " pdb=" CA VAL K 18 " pdb=" CG1 VAL K 18 " pdb=" CG2 VAL K 18 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1475 not shown) Planarity restraints: 1488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN O 39 " 0.062 5.00e-02 4.00e+02 9.42e-02 1.42e+01 pdb=" N PRO O 40 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO O 40 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO O 40 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU f 16 " 0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C LEU f 16 " -0.058 2.00e-02 2.50e+03 pdb=" O LEU f 16 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY f 17 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN M 39 " -0.053 5.00e-02 4.00e+02 8.00e-02 1.02e+01 pdb=" N PRO M 40 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO M 40 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO M 40 " -0.043 5.00e-02 4.00e+02 ... (remaining 1485 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 70 2.48 - 3.09: 5633 3.09 - 3.69: 13365 3.69 - 4.30: 17885 4.30 - 4.90: 27831 Nonbonded interactions: 64784 Sorted by model distance: nonbonded pdb=" O LYS f 53 " pdb=" O ARG a 41 " model vdw 1.880 3.040 nonbonded pdb=" O UNK e 21 " pdb=" CB UNK e 25 " model vdw 1.935 2.752 nonbonded pdb=" O GLU f 13 " pdb=" N GLU f 18 " model vdw 1.956 3.120 nonbonded pdb=" O UNK e 22 " pdb=" CB UNK e 26 " model vdw 1.975 2.752 nonbonded pdb=" CA VAL f 14 " pdb=" O GLU f 18 " model vdw 2.046 3.470 ... (remaining 64779 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'K' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) selection = (chain 'L' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) selection = (chain 'M' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) selection = chain 'N' selection = (chain 'O' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) selection = (chain 'P' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) selection = (chain 'Q' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) selection = (chain 'R' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 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: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.810 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5646 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 : 0.008 0.091 8665 Z= 0.499 Angle : 1.250 15.182 11787 Z= 0.730 Chirality : 0.054 0.237 1478 Planarity : 0.008 0.094 1488 Dihedral : 15.225 71.561 2668 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.88 % Favored : 90.54 % Rotamer: Outliers : 1.18 % Allowed : 19.15 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.59 % 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: -6.05 (0.19), residues: 1036 helix: -4.00 (0.12), residues: 734 sheet: None (None), residues: 0 loop : -3.38 (0.31), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP a 68 HIS 0.007 0.002 HIS a 172 PHE 0.023 0.003 PHE M 29 TYR 0.029 0.003 TYR i 21 ARG 0.013 0.002 ARG a 159 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 310 time to evaluate : 0.819 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLN i 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 49 LEU cc_start: 0.8203 (tt) cc_final: 0.7914 (mm) REVERT: a 121 THR cc_start: 0.4360 (OUTLIER) cc_final: 0.3610 (t) REVERT: a 183 ASN cc_start: 0.6252 (m-40) cc_final: 0.5730 (p0) REVERT: a 203 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7446 (mp0) REVERT: a 209 ILE cc_start: 0.7353 (mm) cc_final: 0.7035 (mm) REVERT: L 66 MET cc_start: 0.2629 (mtt) cc_final: 0.2178 (ppp) REVERT: M 42 LEU cc_start: 0.4778 (OUTLIER) cc_final: 0.4368 (pp) REVERT: N 63 PHE cc_start: 0.6844 (p90) cc_final: 0.6530 (p90) REVERT: O 3 ASP cc_start: 0.6181 (p0) cc_final: 0.5898 (t0) REVERT: O 56 LEU cc_start: 0.8723 (tp) cc_final: 0.8487 (mp) REVERT: P 62 LEU cc_start: 0.6853 (mt) cc_final: 0.6475 (mt) REVERT: Q 25 ILE cc_start: 0.7563 (pt) cc_final: 0.7247 (pt) REVERT: R 62 LEU cc_start: 0.7522 (mm) cc_final: 0.7283 (mm) outliers start: 8 outliers final: 2 residues processed: 314 average time/residue: 0.1703 time to fit residues: 75.3470 Evaluate side-chains 203 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 199 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 0.0870 chunk 96 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 111 optimal weight: 0.7980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 39 ASN a 83 ASN a 97 GLN a 168 HIS a 172 HIS a 210 GLN K 45 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6039 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8665 Z= 0.215 Angle : 0.766 8.522 11787 Z= 0.386 Chirality : 0.040 0.187 1478 Planarity : 0.006 0.062 1488 Dihedral : 6.509 45.741 1306 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.76 % Favored : 92.86 % Rotamer: Outliers : 0.29 % Allowed : 7.07 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -4.64 (0.22), residues: 1036 helix: -2.73 (0.15), residues: 779 sheet: None (None), residues: 0 loop : -3.48 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP 8 9 HIS 0.012 0.002 HIS a 168 PHE 0.032 0.002 PHE M 8 TYR 0.013 0.002 TYR i 21 ARG 0.004 0.001 ARG O 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 248 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 66 TYR cc_start: 0.6640 (t80) cc_final: 0.6104 (t80) REVERT: a 73 MET cc_start: 0.8459 (mmm) cc_final: 0.8126 (mmp) REVERT: a 214 PHE cc_start: 0.6698 (t80) cc_final: 0.6434 (t80) REVERT: L 66 MET cc_start: 0.2820 (mtt) cc_final: 0.2159 (ppp) REVERT: N 32 MET cc_start: 0.8091 (tmm) cc_final: 0.7795 (tmm) REVERT: N 39 ASN cc_start: 0.7600 (t0) cc_final: 0.7308 (t0) REVERT: N 46 LEU cc_start: 0.5921 (mm) cc_final: 0.5585 (mm) REVERT: O 56 LEU cc_start: 0.8932 (tp) cc_final: 0.8505 (mp) REVERT: P 60 MET cc_start: 0.7821 (tpt) cc_final: 0.7557 (tpt) REVERT: Q 44 GLN cc_start: 0.7488 (mp10) cc_final: 0.7224 (mp10) REVERT: R 42 LEU cc_start: 0.7844 (pt) cc_final: 0.7339 (pt) REVERT: R 43 LYS cc_start: 0.7987 (mptt) cc_final: 0.7294 (tmmt) REVERT: R 44 GLN cc_start: 0.7775 (tp-100) cc_final: 0.7521 (tp40) REVERT: R 60 MET cc_start: 0.2539 (mtm) cc_final: 0.1590 (mmm) outliers start: 2 outliers final: 0 residues processed: 250 average time/residue: 0.1528 time to fit residues: 56.0083 Evaluate side-chains 193 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 111 optimal weight: 0.9990 chunk 120 optimal weight: 8.9990 chunk 99 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.9788 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6268 moved from start: 0.5574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8665 Z= 0.206 Angle : 0.712 8.574 11787 Z= 0.356 Chirality : 0.040 0.218 1478 Planarity : 0.005 0.058 1488 Dihedral : 5.819 44.557 1306 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.34 % Favored : 92.37 % Rotamer: Outliers : 0.15 % Allowed : 7.36 % Favored : 92.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.23), residues: 1036 helix: -2.00 (0.16), residues: 796 sheet: None (None), residues: 0 loop : -3.39 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP 8 9 HIS 0.003 0.001 HIS a 172 PHE 0.025 0.002 PHE M 63 TYR 0.017 0.002 TYR i 21 ARG 0.004 0.001 ARG i 26 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 226 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 209 ILE cc_start: 0.7738 (mm) cc_final: 0.7430 (mm) REVERT: M 32 MET cc_start: 0.7621 (tmm) cc_final: 0.7399 (tmm) REVERT: N 32 MET cc_start: 0.8243 (tmm) cc_final: 0.7806 (tmm) REVERT: N 46 LEU cc_start: 0.6099 (mm) cc_final: 0.5649 (mm) REVERT: N 66 MET cc_start: 0.7634 (mmm) cc_final: 0.7299 (mmp) REVERT: O 56 LEU cc_start: 0.9035 (tp) cc_final: 0.8666 (mp) REVERT: Q 8 PHE cc_start: 0.6123 (m-80) cc_final: 0.5908 (m-80) REVERT: R 7 LYS cc_start: 0.7226 (mmtt) cc_final: 0.6847 (ptpt) REVERT: R 42 LEU cc_start: 0.7423 (pt) cc_final: 0.7067 (pt) REVERT: R 44 GLN cc_start: 0.8051 (tp-100) cc_final: 0.7846 (tp40) REVERT: R 60 MET cc_start: 0.4005 (mtp) cc_final: 0.2879 (mmm) REVERT: R 71 ILE cc_start: 0.7693 (tt) cc_final: 0.7032 (tt) outliers start: 1 outliers final: 0 residues processed: 227 average time/residue: 0.1513 time to fit residues: 51.1998 Evaluate side-chains 186 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 58 optimal weight: 0.1980 chunk 12 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 75 optimal weight: 0.7980 chunk 112 optimal weight: 0.0570 chunk 118 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 32 optimal weight: 0.0470 chunk 99 optimal weight: 0.0040 overall best weight: 0.2208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 97 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6165 moved from start: 0.6164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8665 Z= 0.154 Angle : 0.648 7.584 11787 Z= 0.315 Chirality : 0.038 0.321 1478 Planarity : 0.004 0.046 1488 Dihedral : 5.312 42.655 1306 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.85 % Favored : 92.95 % Rotamer: Outliers : 0.15 % Allowed : 3.53 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.25), residues: 1036 helix: -1.40 (0.17), residues: 783 sheet: None (None), residues: 0 loop : -2.82 (0.40), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP 8 9 HIS 0.002 0.000 HIS a 172 PHE 0.027 0.002 PHE O 29 TYR 0.015 0.001 TYR i 21 ARG 0.002 0.000 ARG O 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 233 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: i 46 LEU cc_start: 0.7946 (tp) cc_final: 0.7626 (pp) REVERT: a 46 GLN cc_start: 0.7644 (tt0) cc_final: 0.7320 (tm-30) REVERT: a 209 ILE cc_start: 0.7524 (mm) cc_final: 0.6995 (mm) REVERT: L 45 GLN cc_start: 0.8392 (pt0) cc_final: 0.8068 (pt0) REVERT: N 32 MET cc_start: 0.8112 (tmm) cc_final: 0.7629 (tmm) REVERT: O 56 LEU cc_start: 0.8914 (tp) cc_final: 0.8641 (mp) REVERT: P 56 LEU cc_start: 0.6879 (tp) cc_final: 0.6503 (tt) REVERT: Q 8 PHE cc_start: 0.6063 (m-80) cc_final: 0.5847 (m-80) REVERT: R 7 LYS cc_start: 0.7158 (mmtt) cc_final: 0.6866 (ptpt) REVERT: R 60 MET cc_start: 0.3879 (mtp) cc_final: 0.2835 (mmm) REVERT: R 71 ILE cc_start: 0.7666 (tt) cc_final: 0.7026 (tt) outliers start: 1 outliers final: 0 residues processed: 234 average time/residue: 0.1573 time to fit residues: 53.5679 Evaluate side-chains 190 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 0.9980 chunk 1 optimal weight: 30.0000 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 101 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 60 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 46 GLN ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6340 moved from start: 0.6729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8665 Z= 0.181 Angle : 0.669 6.763 11787 Z= 0.327 Chirality : 0.038 0.249 1478 Planarity : 0.004 0.051 1488 Dihedral : 5.213 43.917 1306 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 0.15 % Allowed : 3.68 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.26), residues: 1036 helix: -1.05 (0.18), residues: 769 sheet: None (None), residues: 0 loop : -2.52 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP 8 9 HIS 0.002 0.001 HIS a 223 PHE 0.028 0.001 PHE M 63 TYR 0.017 0.001 TYR i 21 ARG 0.002 0.001 ARG i 26 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 216 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: i 46 LEU cc_start: 0.8018 (tp) cc_final: 0.7712 (pp) REVERT: a 46 GLN cc_start: 0.7722 (tt0) cc_final: 0.7491 (tt0) REVERT: a 209 ILE cc_start: 0.7466 (mm) cc_final: 0.7090 (mm) REVERT: K 45 GLN cc_start: 0.5955 (pm20) cc_final: 0.5583 (pp30) REVERT: N 32 MET cc_start: 0.8549 (tmm) cc_final: 0.8117 (tmm) REVERT: O 56 LEU cc_start: 0.8931 (tp) cc_final: 0.8671 (mp) REVERT: R 27 THR cc_start: 0.9069 (p) cc_final: 0.8756 (t) REVERT: R 60 MET cc_start: 0.4195 (mtp) cc_final: 0.3915 (tpt) outliers start: 1 outliers final: 0 residues processed: 217 average time/residue: 0.1397 time to fit residues: 45.8856 Evaluate side-chains 186 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 0.2980 chunk 23 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 119 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 62 optimal weight: 0.0570 chunk 114 optimal weight: 0.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6332 moved from start: 0.7052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8665 Z= 0.163 Angle : 0.641 7.522 11787 Z= 0.312 Chirality : 0.038 0.409 1478 Planarity : 0.004 0.047 1488 Dihedral : 4.983 42.443 1306 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -1.94 (0.26), residues: 1036 helix: -0.77 (0.18), residues: 774 sheet: None (None), residues: 0 loop : -2.49 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP 8 9 HIS 0.002 0.001 HIS a 223 PHE 0.027 0.001 PHE M 63 TYR 0.019 0.001 TYR i 21 ARG 0.002 0.000 ARG L 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 0.782 Fit side-chains revert: symmetry clash REVERT: f 76 LYS cc_start: 0.7746 (mmtp) cc_final: 0.7541 (mmtp) REVERT: i 46 LEU cc_start: 0.7783 (tp) cc_final: 0.7505 (pp) REVERT: a 209 ILE cc_start: 0.7406 (mm) cc_final: 0.7072 (mm) REVERT: K 36 TYR cc_start: 0.6842 (t80) cc_final: 0.6356 (t80) REVERT: K 60 MET cc_start: 0.5917 (ppp) cc_final: 0.5425 (ppp) REVERT: L 66 MET cc_start: 0.5583 (mmp) cc_final: 0.3310 (ppp) REVERT: N 32 MET cc_start: 0.8522 (tmm) cc_final: 0.8017 (tmm) REVERT: O 56 LEU cc_start: 0.8936 (tp) cc_final: 0.8712 (mp) REVERT: O 63 PHE cc_start: 0.7690 (t80) cc_final: 0.7439 (t80) REVERT: R 27 THR cc_start: 0.9107 (p) cc_final: 0.8774 (t) REVERT: R 60 MET cc_start: 0.4415 (mtp) cc_final: 0.3725 (tpt) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.1472 time to fit residues: 48.1131 Evaluate side-chains 193 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 10.0000 chunk 67 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 54 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 47 optimal weight: 0.4980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 46 GLN ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6400 moved from start: 0.7556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8665 Z= 0.166 Angle : 0.648 7.102 11787 Z= 0.315 Chirality : 0.038 0.346 1478 Planarity : 0.004 0.047 1488 Dihedral : 4.899 42.173 1306 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -1.69 (0.26), residues: 1036 helix: -0.60 (0.19), residues: 769 sheet: None (None), residues: 0 loop : -2.31 (0.40), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP 8 9 HIS 0.002 0.001 HIS a 223 PHE 0.028 0.001 PHE M 63 TYR 0.018 0.001 TYR i 21 ARG 0.002 0.000 ARG L 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: i 46 LEU cc_start: 0.7781 (tp) cc_final: 0.7535 (pp) REVERT: a 128 PHE cc_start: 0.6824 (m-10) cc_final: 0.6407 (m-80) REVERT: a 209 ILE cc_start: 0.7447 (mm) cc_final: 0.7161 (mm) REVERT: K 3 ASP cc_start: 0.7741 (m-30) cc_final: 0.7178 (m-30) REVERT: K 60 MET cc_start: 0.5891 (ppp) cc_final: 0.5443 (ppp) REVERT: L 44 GLN cc_start: 0.7659 (tt0) cc_final: 0.7180 (pt0) REVERT: L 66 MET cc_start: 0.5628 (mmp) cc_final: 0.5322 (mmm) REVERT: M 71 ILE cc_start: 0.8356 (mm) cc_final: 0.8127 (mm) REVERT: N 32 MET cc_start: 0.8567 (tmm) cc_final: 0.8004 (tmm) REVERT: O 63 PHE cc_start: 0.7918 (t80) cc_final: 0.7594 (t80) REVERT: P 56 LEU cc_start: 0.7246 (tp) cc_final: 0.6934 (tt) REVERT: R 27 THR cc_start: 0.9200 (p) cc_final: 0.8873 (t) REVERT: R 60 MET cc_start: 0.5087 (mtp) cc_final: 0.4395 (tpt) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.1441 time to fit residues: 47.2552 Evaluate side-chains 195 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 2.9990 chunk 35 optimal weight: 0.1980 chunk 23 optimal weight: 0.3980 chunk 22 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 11 optimal weight: 9.9990 chunk 93 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6389 moved from start: 0.7898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8665 Z= 0.151 Angle : 0.633 7.289 11787 Z= 0.308 Chirality : 0.039 0.446 1478 Planarity : 0.004 0.043 1488 Dihedral : 4.758 43.248 1306 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.48 (0.27), residues: 1036 helix: -0.45 (0.19), residues: 780 sheet: None (None), residues: 0 loop : -2.33 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP 8 9 HIS 0.003 0.001 HIS a 172 PHE 0.028 0.001 PHE M 63 TYR 0.017 0.001 TYR i 21 ARG 0.002 0.000 ARG i 26 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: i 46 LEU cc_start: 0.7770 (tp) cc_final: 0.7538 (pp) REVERT: 8 18 MET cc_start: 0.7072 (mtt) cc_final: 0.6720 (mtt) REVERT: a 128 PHE cc_start: 0.6996 (m-10) cc_final: 0.6549 (m-80) REVERT: a 214 PHE cc_start: 0.6802 (t80) cc_final: 0.6189 (t80) REVERT: K 3 ASP cc_start: 0.7876 (m-30) cc_final: 0.6906 (t0) REVERT: K 60 MET cc_start: 0.5831 (ppp) cc_final: 0.5492 (ppp) REVERT: L 66 MET cc_start: 0.5526 (mmp) cc_final: 0.5283 (mmm) REVERT: M 71 ILE cc_start: 0.8254 (mm) cc_final: 0.8036 (mm) REVERT: N 32 MET cc_start: 0.8538 (tmm) cc_final: 0.7987 (tmm) REVERT: O 63 PHE cc_start: 0.7768 (t80) cc_final: 0.7435 (t80) REVERT: R 27 THR cc_start: 0.9168 (p) cc_final: 0.8873 (t) REVERT: R 60 MET cc_start: 0.4784 (mtp) cc_final: 0.4289 (tpt) REVERT: R 63 PHE cc_start: 0.6656 (m-10) cc_final: 0.6371 (m-10) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.1522 time to fit residues: 51.8444 Evaluate side-chains 196 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 48 optimal weight: 0.4980 chunk 86 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 72 optimal weight: 0.3980 chunk 116 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 44 GLN ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6430 moved from start: 0.8121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8665 Z= 0.160 Angle : 0.645 7.684 11787 Z= 0.310 Chirality : 0.039 0.350 1478 Planarity : 0.004 0.042 1488 Dihedral : 4.738 42.291 1306 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.29 (0.27), residues: 1036 helix: -0.37 (0.19), residues: 771 sheet: None (None), residues: 0 loop : -1.95 (0.41), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP 8 9 HIS 0.002 0.001 HIS a 127 PHE 0.028 0.001 PHE M 63 TYR 0.016 0.001 TYR i 21 ARG 0.002 0.000 ARG L 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: i 46 LEU cc_start: 0.7946 (tp) cc_final: 0.7546 (pp) REVERT: 8 18 MET cc_start: 0.7296 (mtt) cc_final: 0.7031 (mtt) REVERT: a 128 PHE cc_start: 0.6880 (m-10) cc_final: 0.6431 (m-80) REVERT: a 209 ILE cc_start: 0.7868 (mm) cc_final: 0.7665 (mm) REVERT: a 214 PHE cc_start: 0.6791 (t80) cc_final: 0.6218 (t80) REVERT: K 3 ASP cc_start: 0.7876 (m-30) cc_final: 0.6824 (t0) REVERT: K 60 MET cc_start: 0.5869 (ppp) cc_final: 0.5492 (ppp) REVERT: L 8 PHE cc_start: 0.5608 (m-80) cc_final: 0.5249 (m-80) REVERT: L 66 MET cc_start: 0.5512 (mmp) cc_final: 0.5247 (mmm) REVERT: M 71 ILE cc_start: 0.8159 (mm) cc_final: 0.7944 (mm) REVERT: N 32 MET cc_start: 0.8546 (tmm) cc_final: 0.7987 (tmm) REVERT: O 63 PHE cc_start: 0.8029 (t80) cc_final: 0.7609 (t80) REVERT: P 56 LEU cc_start: 0.7274 (tp) cc_final: 0.7046 (tt) REVERT: R 27 THR cc_start: 0.9232 (p) cc_final: 0.8940 (t) REVERT: R 60 MET cc_start: 0.4861 (mtp) cc_final: 0.4322 (tpt) REVERT: R 63 PHE cc_start: 0.6679 (m-10) cc_final: 0.6296 (m-10) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.1603 time to fit residues: 52.0814 Evaluate side-chains 186 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 81 optimal weight: 0.0370 chunk 122 optimal weight: 20.0000 chunk 112 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 10 optimal weight: 9.9990 chunk 75 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 103 optimal weight: 0.5980 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6430 moved from start: 0.8365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8665 Z= 0.159 Angle : 0.656 8.585 11787 Z= 0.314 Chirality : 0.039 0.288 1478 Planarity : 0.004 0.042 1488 Dihedral : 4.672 41.246 1306 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.16 (0.27), residues: 1036 helix: -0.27 (0.19), residues: 779 sheet: None (None), residues: 0 loop : -2.00 (0.42), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP 8 9 HIS 0.002 0.001 HIS a 127 PHE 0.029 0.001 PHE O 29 TYR 0.023 0.001 TYR K 49 ARG 0.002 0.000 ARG i 26 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: i 46 LEU cc_start: 0.7943 (tp) cc_final: 0.7498 (pp) REVERT: 8 18 MET cc_start: 0.7332 (mtt) cc_final: 0.7059 (mtt) REVERT: a 14 MET cc_start: 0.6722 (ppp) cc_final: 0.6484 (ppp) REVERT: a 128 PHE cc_start: 0.6967 (m-10) cc_final: 0.6701 (m-80) REVERT: a 209 ILE cc_start: 0.7829 (mm) cc_final: 0.7616 (mm) REVERT: a 214 PHE cc_start: 0.6778 (t80) cc_final: 0.6177 (t80) REVERT: K 3 ASP cc_start: 0.7882 (m-30) cc_final: 0.6871 (t0) REVERT: N 32 MET cc_start: 0.8590 (tmm) cc_final: 0.8062 (tmm) REVERT: N 39 ASN cc_start: 0.8312 (t0) cc_final: 0.8075 (t0) REVERT: O 63 PHE cc_start: 0.8110 (t80) cc_final: 0.7681 (t80) REVERT: Q 64 CYS cc_start: 0.8613 (m) cc_final: 0.8398 (m) REVERT: R 27 THR cc_start: 0.9277 (p) cc_final: 0.8978 (t) REVERT: R 60 MET cc_start: 0.4707 (mtp) cc_final: 0.4406 (tpt) REVERT: R 63 PHE cc_start: 0.6766 (m-10) cc_final: 0.6360 (m-10) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.1457 time to fit residues: 46.6705 Evaluate side-chains 180 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 97 optimal weight: 0.7980 chunk 40 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 10 GLN a 66 GLN ** a 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 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 = 0.4131 r_free = 0.4131 target = 0.149005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.119801 restraints weight = 20389.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.122015 restraints weight = 13446.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.123306 restraints weight = 10224.922| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.8910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8665 Z= 0.271 Angle : 0.781 8.888 11787 Z= 0.384 Chirality : 0.042 0.231 1478 Planarity : 0.005 0.053 1488 Dihedral : 5.546 42.858 1306 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.26), residues: 1036 helix: -0.67 (0.19), residues: 755 sheet: None (None), residues: 0 loop : -2.23 (0.39), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP 8 9 HIS 0.005 0.002 HIS a 127 PHE 0.036 0.002 PHE O 29 TYR 0.017 0.002 TYR M 49 ARG 0.004 0.001 ARG i 26 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1831.69 seconds wall clock time: 33 minutes 13.89 seconds (1993.89 seconds total)