Starting phenix.real_space_refine on Fri Feb 16 13:46:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wfe_8827/02_2024/5wfe_8827.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wfe_8827/02_2024/5wfe_8827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wfe_8827/02_2024/5wfe_8827.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wfe_8827/02_2024/5wfe_8827.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wfe_8827/02_2024/5wfe_8827.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wfe_8827/02_2024/5wfe_8827.pdb" } resolution = 3.64 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.081 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 208 5.49 5 S 40 5.16 5 C 9220 2.51 5 N 2771 2.21 5 O 3284 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 95": "NH1" <-> "NH2" Residue "A ARG 131": "NH1" <-> "NH2" Residue "A ARG 132": "NH1" <-> "NH2" Residue "A ARG 138": "NH1" <-> "NH2" Residue "B PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B ARG 132": "NH1" <-> "NH2" Residue "B ARG 138": "NH1" <-> "NH2" Residue "C ARG 95": "NH1" <-> "NH2" Residue "C ARG 131": "NH1" <-> "NH2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C ARG 138": "NH1" <-> "NH2" Residue "D PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 132": "NH1" <-> "NH2" Residue "D ARG 138": "NH1" <-> "NH2" Residue "E ARG 77": "NH1" <-> "NH2" Residue "F ARG 78": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15523 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2018 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 14, 'TRANS': 247} Chain breaks: 1 Chain: "B" Number of atoms: 2157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2157 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 17, 'TRANS': 261} Chain: "C" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1964 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 12, 'TRANS': 243} Chain breaks: 1 Chain: "D" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2096 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 15, 'TRANS': 256} Chain: "E" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 739 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "F" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 739 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "G" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 578 Classifications: {'DNA': 28} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 27} Chain: "H" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 907 Classifications: {'DNA': 45} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 44} Chain: "I" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1570 Classifications: {'DNA': 77} Link IDs: {'rna3p': 76} Chain: "J" Number of atoms: 1244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1244 Classifications: {'DNA': 60} Link IDs: {'rna3p': 59} Chain: "K" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 769 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 742 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 88} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 8.66, per 1000 atoms: 0.56 Number of scatterers: 15523 At special positions: 0 Unit cell: (120.91, 128.4, 196.88, 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 40 16.00 P 208 15.00 O 3284 8.00 N 2771 7.00 C 9220 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.03 Conformation dependent library (CDL) restraints added in 2.1 seconds 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2652 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 9 sheets defined 54.1% alpha, 14.9% beta 94 base pairs and 161 stacking pairs defined. Time for finding SS restraints: 6.96 Creating SS restraints... Processing helix chain 'A' and resid 62 through 71 Processing helix chain 'A' and resid 80 through 83 Processing helix chain 'A' and resid 95 through 108 Processing helix chain 'A' and resid 108 through 124 Processing helix chain 'A' and resid 133 through 157 Processing helix chain 'A' and resid 175 through 199 Processing helix chain 'A' and resid 213 through 223 removed outlier: 3.756A pdb=" N ILE A 223 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 239 Processing helix chain 'A' and resid 242 through 259 removed outlier: 3.790A pdb=" N GLU A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 274 removed outlier: 4.409A pdb=" N ILE A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Proline residue: A 266 - end of helix Processing helix chain 'B' and resid 45 through 47 No H-bonds generated for 'chain 'B' and resid 45 through 47' Processing helix chain 'B' and resid 62 through 71 Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 95 through 108 removed outlier: 4.121A pdb=" N LEU B 99 " --> pdb=" O ARG B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 124 Processing helix chain 'B' and resid 133 through 157 Processing helix chain 'B' and resid 166 through 170 removed outlier: 3.592A pdb=" N ASP B 169 " --> pdb=" O ASP B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 199 Processing helix chain 'B' and resid 213 through 239 removed outlier: 3.984A pdb=" N ILE B 223 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N PHE B 225 " --> pdb=" O ASP B 221 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ASP B 226 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THR B 227 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N VAL B 229 " --> pdb=" O PHE B 225 " (cutoff:3.500A) Proline residue: B 230 - end of helix Processing helix chain 'B' and resid 242 through 259 removed outlier: 3.521A pdb=" N GLU B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 274 removed outlier: 4.136A pdb=" N ILE B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Proline residue: B 266 - end of helix removed outlier: 3.757A pdb=" N ALA B 274 " --> pdb=" O ASP B 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 71 Processing helix chain 'C' and resid 80 through 83 Processing helix chain 'C' and resid 95 through 108 removed outlier: 3.670A pdb=" N LEU C 99 " --> pdb=" O ARG C 95 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP C 108 " --> pdb=" O LYS C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 124 Processing helix chain 'C' and resid 133 through 156 Processing helix chain 'C' and resid 175 through 199 Processing helix chain 'C' and resid 213 through 223 removed outlier: 3.883A pdb=" N ILE C 223 " --> pdb=" O ILE C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 239 Processing helix chain 'C' and resid 242 through 259 removed outlier: 3.630A pdb=" N GLU C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 274 removed outlier: 4.505A pdb=" N ILE C 265 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Proline residue: C 266 - end of helix Processing helix chain 'D' and resid 10 through 14 removed outlier: 3.595A pdb=" N ARG D 14 " --> pdb=" O LEU D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 47 No H-bonds generated for 'chain 'D' and resid 45 through 47' Processing helix chain 'D' and resid 62 through 71 Processing helix chain 'D' and resid 80 through 82 No H-bonds generated for 'chain 'D' and resid 80 through 82' Processing helix chain 'D' and resid 95 through 108 removed outlier: 3.766A pdb=" N ASP D 108 " --> pdb=" O LYS D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 125 Processing helix chain 'D' and resid 133 through 157 removed outlier: 3.536A pdb=" N LEU D 137 " --> pdb=" O SER D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 170 removed outlier: 3.566A pdb=" N ASP D 169 " --> pdb=" O ASP D 166 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TRP D 170 " --> pdb=" O PRO D 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 166 through 170' Processing helix chain 'D' and resid 175 through 199 Processing helix chain 'D' and resid 213 through 239 removed outlier: 3.764A pdb=" N ILE D 223 " --> pdb=" O ILE D 219 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N PHE D 225 " --> pdb=" O ASP D 221 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ASP D 226 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR D 227 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N VAL D 229 " --> pdb=" O PHE D 225 " (cutoff:3.500A) Proline residue: D 230 - end of helix Processing helix chain 'D' and resid 242 through 259 removed outlier: 3.971A pdb=" N GLU D 246 " --> pdb=" O GLU D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 274 removed outlier: 3.986A pdb=" N LYS D 263 " --> pdb=" O LYS D 259 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE D 265 " --> pdb=" O LEU D 261 " (cutoff:3.500A) Proline residue: D 266 - end of helix removed outlier: 4.043A pdb=" N ALA D 274 " --> pdb=" O ASP D 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 23 removed outlier: 3.735A pdb=" N ARG E 16 " --> pdb=" O PRO E 12 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TRP E 22 " --> pdb=" O ARG E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 51 removed outlier: 3.523A pdb=" N ALA E 51 " --> pdb=" O ILE E 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 23 removed outlier: 3.634A pdb=" N ARG F 16 " --> pdb=" O PRO F 12 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TRP F 22 " --> pdb=" O ARG F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 51 Processing helix chain 'K' and resid 4 through 17 Processing helix chain 'K' and resid 19 through 40 removed outlier: 3.514A pdb=" N VAL K 27 " --> pdb=" O ALA K 23 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE K 34 " --> pdb=" O PHE K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 93 removed outlier: 4.225A pdb=" N ASN K 93 " --> pdb=" O SER K 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 14 removed outlier: 3.727A pdb=" N ARG L 9 " --> pdb=" O GLU L 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 18 through 39 Processing helix chain 'L' and resid 83 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 20 removed outlier: 5.809A pdb=" N ILE A 18 " --> pdb=" O MET A 53 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU A 75 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER A 88 " --> pdb=" O GLY B 89 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY B 89 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU B 74 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N VAL B 15 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ILE B 52 " --> pdb=" O VAL B 15 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N MET B 17 " --> pdb=" O ILE B 52 " (cutoff:3.500A) removed outlier: 9.804A pdb=" N LEU B 54 " --> pdb=" O MET B 17 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N PHE B 19 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 35 removed outlier: 7.215A pdb=" N ILE A 25 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N VAL B 27 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N HIS B 43 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N VAL E 89 " --> pdb=" O HIS B 43 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 17 through 20 removed outlier: 6.093A pdb=" N ILE C 18 " --> pdb=" O MET C 53 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N LEU C 75 " --> pdb=" O GLY C 89 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU D 75 " --> pdb=" O SER D 88 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N SER D 16 " --> pdb=" O CYS D 51 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N MET D 53 " --> pdb=" O SER D 16 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ILE D 18 " --> pdb=" O MET D 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 32 through 35 removed outlier: 7.472A pdb=" N ILE C 25 " --> pdb=" O SER C 61 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N VAL D 27 " --> pdb=" O SER D 61 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS D 43 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL F 89 " --> pdb=" O HIS D 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 24 through 27 removed outlier: 3.707A pdb=" N VAL E 26 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL E 30 " --> pdb=" O VAL E 26 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N MET E 3 " --> pdb=" O ALA E 61 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 24 through 27 removed outlier: 6.836A pdb=" N VAL F 30 " --> pdb=" O VAL F 26 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N MET F 3 " --> pdb=" O ALA F 61 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 44 through 46 removed outlier: 3.734A pdb=" N ARG K 76 " --> pdb=" O LYS K 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 43 through 45 removed outlier: 4.049A pdb=" N LYS L 75 " --> pdb=" O ARG L 56 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 60 through 62 666 hydrogen bonds defined for protein. 1935 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 221 hydrogen bonds 432 hydrogen bond angles 0 basepair planarities 94 basepair parallelities 161 stacking parallelities Total time for adding SS restraints: 5.72 Time building geometry restraints manager: 8.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3566 1.33 - 1.45: 4073 1.45 - 1.57: 8138 1.57 - 1.69: 414 1.69 - 1.81: 64 Bond restraints: 16255 Sorted by residual: bond pdb=" N LYS F 38 " pdb=" CA LYS F 38 " ideal model delta sigma weight residual 1.457 1.407 0.050 1.29e-02 6.01e+03 1.52e+01 bond pdb=" C ALA F 37 " pdb=" N LYS F 38 " ideal model delta sigma weight residual 1.332 1.297 0.035 1.40e-02 5.10e+03 6.27e+00 bond pdb=" C3' DG I 6 " pdb=" O3' DG I 6 " ideal model delta sigma weight residual 1.422 1.477 -0.055 3.00e-02 1.11e+03 3.31e+00 bond pdb=" C GLN A 90 " pdb=" O GLN A 90 " ideal model delta sigma weight residual 1.233 1.224 0.009 4.80e-03 4.34e+04 3.19e+00 bond pdb=" C3' DC H 37 " pdb=" O3' DC H 37 " ideal model delta sigma weight residual 1.422 1.474 -0.052 3.00e-02 1.11e+03 3.03e+00 ... (remaining 16250 not shown) Histogram of bond angle deviations from ideal: 97.56 - 104.84: 1063 104.84 - 112.13: 8661 112.13 - 119.42: 4939 119.42 - 126.70: 7506 126.70 - 133.99: 749 Bond angle restraints: 22918 Sorted by residual: angle pdb=" C ALA F 37 " pdb=" N LYS F 38 " pdb=" CA LYS F 38 " ideal model delta sigma weight residual 121.54 115.20 6.34 1.91e+00 2.74e-01 1.10e+01 angle pdb=" C GLU E 52 " pdb=" CA GLU E 52 " pdb=" CB GLU E 52 " ideal model delta sigma weight residual 114.40 110.60 3.80 1.25e+00 6.40e-01 9.24e+00 angle pdb=" C ALA B 273 " pdb=" N ALA B 274 " pdb=" CA ALA B 274 " ideal model delta sigma weight residual 120.38 124.68 -4.30 1.46e+00 4.69e-01 8.67e+00 angle pdb=" C3' DC H 37 " pdb=" O3' DC H 37 " pdb=" P DG H 38 " ideal model delta sigma weight residual 120.20 124.58 -4.38 1.50e+00 4.44e-01 8.53e+00 angle pdb=" C3' DT J 33 " pdb=" C2' DT J 33 " pdb=" C1' DT J 33 " ideal model delta sigma weight residual 101.60 97.56 4.04 1.50e+00 4.44e-01 7.26e+00 ... (remaining 22913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.61: 8202 34.61 - 69.23: 1031 69.23 - 103.84: 27 103.84 - 138.45: 2 138.45 - 173.07: 6 Dihedral angle restraints: 9268 sinusoidal: 5138 harmonic: 4130 Sorted by residual: dihedral pdb=" CA ARG B 95 " pdb=" C ARG B 95 " pdb=" N SER B 96 " pdb=" CA SER B 96 " ideal model delta harmonic sigma weight residual -180.00 -151.58 -28.42 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" C4' DC I 17 " pdb=" C3' DC I 17 " pdb=" O3' DC I 17 " pdb=" P DA I 18 " ideal model delta sinusoidal sigma weight residual -140.00 33.07 -173.07 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT H 28 " pdb=" C3' DT H 28 " pdb=" O3' DT H 28 " pdb=" P DG H 29 " ideal model delta sinusoidal sigma weight residual 220.00 48.62 171.38 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 9265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1653 0.031 - 0.062: 664 0.062 - 0.093: 192 0.093 - 0.125: 83 0.125 - 0.156: 10 Chirality restraints: 2602 Sorted by residual: chirality pdb=" P DG H 38 " pdb=" OP1 DG H 38 " pdb=" OP2 DG H 38 " pdb=" O5' DG H 38 " both_signs ideal model delta sigma weight residual True 2.35 -2.50 -0.16 2.00e-01 2.50e+01 6.06e-01 chirality pdb=" CB ILE B 176 " pdb=" CA ILE B 176 " pdb=" CG1 ILE B 176 " pdb=" CG2 ILE B 176 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.68e-01 chirality pdb=" C1' DT J 33 " pdb=" O4' DT J 33 " pdb=" C2' DT J 33 " pdb=" N1 DT J 33 " both_signs ideal model delta sigma weight residual False 2.47 2.32 0.15 2.00e-01 2.50e+01 5.40e-01 ... (remaining 2599 not shown) Planarity restraints: 2209 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 166 " 0.047 5.00e-02 4.00e+02 7.16e-02 8.20e+00 pdb=" N PRO A 167 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 167 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 167 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 45 " -0.024 2.00e-02 2.50e+03 1.21e-02 4.02e+00 pdb=" N9 DA I 45 " 0.030 2.00e-02 2.50e+03 pdb=" C8 DA I 45 " 0.000 2.00e-02 2.50e+03 pdb=" N7 DA I 45 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA I 45 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 45 " -0.006 2.00e-02 2.50e+03 pdb=" N6 DA I 45 " -0.001 2.00e-02 2.50e+03 pdb=" N1 DA I 45 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DA I 45 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DA I 45 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DA I 45 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 38 " 0.009 2.00e-02 2.50e+03 1.79e-02 3.20e+00 pdb=" C LYS F 38 " -0.031 2.00e-02 2.50e+03 pdb=" O LYS F 38 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE F 39 " 0.010 2.00e-02 2.50e+03 ... (remaining 2206 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 95 2.49 - 3.09: 10815 3.09 - 3.70: 27152 3.70 - 4.30: 37948 4.30 - 4.90: 56901 Nonbonded interactions: 132911 Sorted by model distance: nonbonded pdb=" N3 DT J 29 " pdb=" CB PRO L 64 " model vdw 1.891 3.520 nonbonded pdb=" O2 DC I 32 " pdb=" N2 DG J 41 " model vdw 2.018 2.496 nonbonded pdb=" N2 DG H 38 " pdb=" O2 DC I 10 " model vdw 2.023 2.496 nonbonded pdb=" C2 DT J 29 " pdb=" CB PRO L 64 " model vdw 2.091 3.660 nonbonded pdb=" N7 DG I 57 " pdb=" N4 DC I 58 " model vdw 2.118 2.600 ... (remaining 132906 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 16 through 167 or resid 174 through 275)) selection = (chain 'B' and (resid 16 through 167 or resid 174 through 275)) selection = (chain 'C' and resid 16 through 275) selection = (chain 'D' and (resid 16 through 167 or resid 174 through 275)) } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.400 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 49.970 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 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 : 0.004 0.055 16255 Z= 0.215 Angle : 0.661 9.228 22918 Z= 0.395 Chirality : 0.039 0.156 2602 Planarity : 0.005 0.072 2209 Dihedral : 23.005 173.065 6616 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.63 % Favored : 95.30 % Rotamer: Outliers : 0.09 % Allowed : 0.77 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.79 (0.19), residues: 1427 helix: -0.66 (0.16), residues: 707 sheet: -0.64 (0.31), residues: 235 loop : -2.08 (0.24), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 77 HIS 0.002 0.001 HIS A 62 PHE 0.021 0.002 PHE B 19 TYR 0.020 0.002 TYR D 149 ARG 0.009 0.001 ARG E 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 417 time to evaluate : 1.609 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: A 53 MET cc_start: 0.8814 (mmt) cc_final: 0.8332 (mmt) REVERT: A 109 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7741 (mm-30) REVERT: A 110 ASP cc_start: 0.8680 (m-30) cc_final: 0.8411 (t0) REVERT: A 121 GLU cc_start: 0.8054 (tt0) cc_final: 0.7713 (tm-30) REVERT: A 131 ARG cc_start: 0.8117 (mtt180) cc_final: 0.7554 (mtm110) REVERT: A 164 ARG cc_start: 0.9005 (mtt180) cc_final: 0.8408 (ptp90) REVERT: A 179 CYS cc_start: 0.8479 (m) cc_final: 0.8130 (p) REVERT: A 192 GLU cc_start: 0.6924 (tt0) cc_final: 0.6690 (tt0) REVERT: A 235 ILE cc_start: 0.8314 (mt) cc_final: 0.8028 (mp) REVERT: A 237 ARG cc_start: 0.8445 (ttp80) cc_final: 0.8230 (tpt-90) REVERT: A 246 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8535 (tp30) REVERT: A 263 LYS cc_start: 0.7593 (mtmt) cc_final: 0.7218 (mmtt) REVERT: B 108 ASP cc_start: 0.7472 (t0) cc_final: 0.7265 (t0) REVERT: B 119 MET cc_start: 0.8415 (mtt) cc_final: 0.7428 (tmm) REVERT: B 154 LYS cc_start: 0.9132 (tttp) cc_final: 0.8886 (mmtm) REVERT: C 54 LEU cc_start: 0.8702 (mt) cc_final: 0.8465 (mp) REVERT: C 55 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8051 (mt-10) REVERT: C 74 LEU cc_start: 0.8414 (tp) cc_final: 0.8083 (pp) REVERT: C 165 TYR cc_start: 0.7439 (p90) cc_final: 0.6297 (p90) REVERT: C 178 GLN cc_start: 0.8433 (tt0) cc_final: 0.8200 (tp-100) REVERT: D 16 SER cc_start: 0.8971 (t) cc_final: 0.8294 (p) REVERT: D 53 MET cc_start: 0.8547 (mmt) cc_final: 0.8324 (mmm) REVERT: D 98 LYS cc_start: 0.8460 (mttt) cc_final: 0.7944 (mptt) REVERT: D 237 ARG cc_start: 0.7992 (ttp80) cc_final: 0.7298 (ttm170) REVERT: D 264 LEU cc_start: 0.7297 (mt) cc_final: 0.7079 (mt) REVERT: E 45 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8223 (tm-30) REVERT: F 9 GLU cc_start: 0.4715 (tt0) cc_final: 0.4475 (mm-30) REVERT: F 31 TYR cc_start: 0.7746 (m-80) cc_final: 0.7407 (m-80) REVERT: F 38 LYS cc_start: 0.6572 (OUTLIER) cc_final: 0.6193 (ptpt) REVERT: K 80 THR cc_start: 0.8072 (p) cc_final: 0.7422 (t) REVERT: K 86 LYS cc_start: 0.9046 (tttp) cc_final: 0.8833 (mtpt) REVERT: L 33 MET cc_start: 0.8150 (mtp) cc_final: 0.7264 (mtp) outliers start: 1 outliers final: 0 residues processed: 418 average time/residue: 0.3457 time to fit residues: 196.7754 Evaluate side-chains 226 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 225 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 8.9990 chunk 121 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 chunk 48 optimal weight: 0.3980 chunk 76 optimal weight: 6.9990 chunk 93 optimal weight: 40.0000 chunk 145 optimal weight: 7.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 278 GLN B 155 GLN B 177 ASN C 90 GLN D 7 ASN E 10 ASN K 59 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.082 16255 Z= 0.592 Angle : 0.892 16.795 22918 Z= 0.480 Chirality : 0.048 0.213 2602 Planarity : 0.007 0.122 2209 Dihedral : 28.568 179.561 3941 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 25.49 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.27 % Favored : 95.59 % Rotamer: Outliers : 3.84 % Allowed : 13.04 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.08 (0.21), residues: 1427 helix: 0.10 (0.18), residues: 716 sheet: -0.47 (0.32), residues: 232 loop : -1.99 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 160 HIS 0.012 0.002 HIS B 62 PHE 0.033 0.003 PHE C 215 TYR 0.026 0.003 TYR A 200 ARG 0.008 0.001 ARG F 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 224 time to evaluate : 1.361 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: A 53 MET cc_start: 0.8714 (mmt) cc_final: 0.8497 (mmm) REVERT: A 110 ASP cc_start: 0.8777 (m-30) cc_final: 0.8349 (t0) REVERT: A 131 ARG cc_start: 0.8334 (mtt180) cc_final: 0.7698 (mtm110) REVERT: A 164 ARG cc_start: 0.8975 (mtt180) cc_final: 0.8651 (ptp90) REVERT: A 237 ARG cc_start: 0.8590 (ttp80) cc_final: 0.8297 (tpt-90) REVERT: B 108 ASP cc_start: 0.7474 (t0) cc_final: 0.7234 (t0) REVERT: B 119 MET cc_start: 0.8395 (mtt) cc_final: 0.7340 (tmm) REVERT: B 154 LYS cc_start: 0.9161 (tttp) cc_final: 0.8908 (mmtm) REVERT: B 178 GLN cc_start: 0.8165 (mt0) cc_final: 0.7716 (mp10) REVERT: B 187 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.6926 (tp) REVERT: C 74 LEU cc_start: 0.8678 (tp) cc_final: 0.8346 (pp) REVERT: C 112 ARG cc_start: 0.7531 (ttt-90) cc_final: 0.7124 (ttm-80) REVERT: C 165 TYR cc_start: 0.7011 (p90) cc_final: 0.6672 (p90) REVERT: C 177 ASN cc_start: 0.9294 (OUTLIER) cc_final: 0.8638 (t0) REVERT: C 178 GLN cc_start: 0.8215 (tt0) cc_final: 0.7823 (tp-100) REVERT: D 98 LYS cc_start: 0.8283 (mttt) cc_final: 0.7995 (mttp) REVERT: D 117 ARG cc_start: 0.8989 (mtp85) cc_final: 0.8710 (mmm-85) REVERT: D 264 LEU cc_start: 0.7403 (mt) cc_final: 0.6984 (mt) REVERT: E 45 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8181 (tm-30) REVERT: F 9 GLU cc_start: 0.4917 (tt0) cc_final: 0.4694 (mm-30) REVERT: F 50 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6614 (mm) REVERT: F 53 GLU cc_start: 0.8301 (tt0) cc_final: 0.7753 (tm-30) REVERT: K 5 LYS cc_start: 0.9008 (pptt) cc_final: 0.8706 (pptt) REVERT: K 13 PHE cc_start: 0.8256 (t80) cc_final: 0.8033 (t80) REVERT: L 76 TYR cc_start: 0.7900 (m-80) cc_final: 0.6656 (t80) outliers start: 45 outliers final: 28 residues processed: 251 average time/residue: 0.3346 time to fit residues: 115.7358 Evaluate side-chains 215 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 184 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain F residue 3 MET Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 34 ILE Chi-restraints excluded: chain K residue 93 ASN Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 26 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 145 optimal weight: 0.4980 chunk 157 optimal weight: 9.9990 chunk 129 optimal weight: 8.9990 chunk 144 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16255 Z= 0.240 Angle : 0.688 11.603 22918 Z= 0.377 Chirality : 0.041 0.173 2602 Planarity : 0.005 0.102 2209 Dihedral : 28.371 179.348 3937 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 19.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.50 % Allowed : 14.41 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.21), residues: 1427 helix: 0.81 (0.18), residues: 717 sheet: -0.40 (0.33), residues: 221 loop : -1.70 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 44 HIS 0.005 0.001 HIS L 32 PHE 0.020 0.002 PHE C 215 TYR 0.018 0.002 TYR C 101 ARG 0.009 0.001 ARG K 76 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 222 time to evaluate : 1.463 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: A 53 MET cc_start: 0.8612 (mmt) cc_final: 0.8360 (mmm) REVERT: A 110 ASP cc_start: 0.8670 (m-30) cc_final: 0.8277 (t0) REVERT: A 131 ARG cc_start: 0.8287 (mtt180) cc_final: 0.7656 (mtm110) REVERT: A 164 ARG cc_start: 0.8938 (mtt180) cc_final: 0.8697 (ptp-170) REVERT: A 179 CYS cc_start: 0.8361 (m) cc_final: 0.8010 (p) REVERT: B 108 ASP cc_start: 0.7167 (t0) cc_final: 0.6893 (t0) REVERT: B 119 MET cc_start: 0.8295 (mtt) cc_final: 0.7116 (tmm) REVERT: B 154 LYS cc_start: 0.9159 (tttp) cc_final: 0.8879 (mmtm) REVERT: B 178 GLN cc_start: 0.8081 (mt0) cc_final: 0.7587 (mp10) REVERT: C 74 LEU cc_start: 0.8560 (tp) cc_final: 0.8253 (pp) REVERT: C 112 ARG cc_start: 0.7374 (ttt-90) cc_final: 0.7136 (ttm170) REVERT: C 165 TYR cc_start: 0.6923 (p90) cc_final: 0.6656 (p90) REVERT: C 177 ASN cc_start: 0.9350 (OUTLIER) cc_final: 0.8675 (t0) REVERT: C 178 GLN cc_start: 0.8253 (tt0) cc_final: 0.8015 (tp-100) REVERT: C 191 THR cc_start: 0.8504 (OUTLIER) cc_final: 0.8227 (p) REVERT: D 61 SER cc_start: 0.8768 (OUTLIER) cc_final: 0.8429 (p) REVERT: D 98 LYS cc_start: 0.8320 (mttt) cc_final: 0.7999 (mttp) REVERT: D 117 ARG cc_start: 0.8956 (mtp85) cc_final: 0.8734 (mmm-85) REVERT: D 264 LEU cc_start: 0.7353 (mt) cc_final: 0.6934 (mt) REVERT: E 1 MET cc_start: 0.5046 (mmm) cc_final: 0.4817 (mmm) REVERT: E 22 TRP cc_start: 0.7151 (m-90) cc_final: 0.6909 (m-10) REVERT: E 45 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8053 (tm-30) REVERT: E 58 MET cc_start: 0.7684 (ttp) cc_final: 0.7395 (tmm) REVERT: F 53 GLU cc_start: 0.8285 (tt0) cc_final: 0.7783 (tm-30) REVERT: F 55 ASN cc_start: 0.6434 (OUTLIER) cc_final: 0.5733 (p0) REVERT: K 5 LYS cc_start: 0.8913 (pptt) cc_final: 0.8533 (pptt) REVERT: K 8 MET cc_start: 0.8628 (mmp) cc_final: 0.8408 (mmp) REVERT: K 86 LYS cc_start: 0.8633 (mtmt) cc_final: 0.8325 (mtmt) REVERT: L 1 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7297 (ttt) REVERT: L 27 LYS cc_start: 0.8679 (mttm) cc_final: 0.8385 (mtmm) REVERT: L 28 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8291 (mm-30) outliers start: 41 outliers final: 21 residues processed: 245 average time/residue: 0.3319 time to fit residues: 113.4315 Evaluate side-chains 226 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 200 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 55 ASN Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain L residue 1 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 4.9990 chunk 109 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 146 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16255 Z= 0.292 Angle : 0.688 11.571 22918 Z= 0.376 Chirality : 0.040 0.154 2602 Planarity : 0.005 0.088 2209 Dihedral : 28.157 178.797 3937 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.50 % Allowed : 15.86 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.18 (0.21), residues: 1427 helix: 0.99 (0.18), residues: 718 sheet: -0.48 (0.33), residues: 221 loop : -1.58 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 77 HIS 0.006 0.001 HIS L 32 PHE 0.017 0.002 PHE C 215 TYR 0.024 0.002 TYR A 149 ARG 0.003 0.001 ARG K 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 219 time to evaluate : 1.593 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: A 53 MET cc_start: 0.8642 (mmt) cc_final: 0.8396 (mmm) REVERT: A 66 ARG cc_start: 0.7800 (ttt-90) cc_final: 0.7355 (mtm110) REVERT: A 110 ASP cc_start: 0.8702 (m-30) cc_final: 0.8318 (t0) REVERT: A 131 ARG cc_start: 0.8297 (mtt180) cc_final: 0.7641 (ptp-110) REVERT: A 164 ARG cc_start: 0.8991 (mtt180) cc_final: 0.8438 (ptp-110) REVERT: A 179 CYS cc_start: 0.8560 (m) cc_final: 0.7949 (p) REVERT: B 108 ASP cc_start: 0.7165 (t0) cc_final: 0.6874 (t0) REVERT: B 119 MET cc_start: 0.8304 (mtt) cc_final: 0.7147 (tmm) REVERT: B 154 LYS cc_start: 0.9176 (tttp) cc_final: 0.8904 (mmtm) REVERT: B 178 GLN cc_start: 0.8004 (mt0) cc_final: 0.7459 (mp10) REVERT: C 74 LEU cc_start: 0.8674 (tp) cc_final: 0.8283 (pp) REVERT: C 112 ARG cc_start: 0.7370 (ttt-90) cc_final: 0.7080 (ttm170) REVERT: C 165 TYR cc_start: 0.6778 (p90) cc_final: 0.6537 (p90) REVERT: C 177 ASN cc_start: 0.9387 (m-40) cc_final: 0.8837 (t0) REVERT: C 191 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.8218 (p) REVERT: D 61 SER cc_start: 0.8786 (OUTLIER) cc_final: 0.8445 (p) REVERT: D 98 LYS cc_start: 0.8331 (mttt) cc_final: 0.8039 (mttp) REVERT: D 117 ARG cc_start: 0.8964 (mtp85) cc_final: 0.8694 (mmm-85) REVERT: D 264 LEU cc_start: 0.7499 (mt) cc_final: 0.7054 (mt) REVERT: E 1 MET cc_start: 0.4947 (mmm) cc_final: 0.4629 (mmm) REVERT: E 3 MET cc_start: 0.6123 (ttp) cc_final: 0.5783 (ttp) REVERT: E 9 GLU cc_start: 0.6410 (mt-10) cc_final: 0.6077 (mp0) REVERT: E 22 TRP cc_start: 0.7293 (m-90) cc_final: 0.6864 (m-10) REVERT: E 42 MET cc_start: 0.8888 (tmm) cc_final: 0.8306 (tmm) REVERT: E 45 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8056 (tm-30) REVERT: F 42 MET cc_start: 0.8225 (tmm) cc_final: 0.8003 (ppp) REVERT: F 52 GLU cc_start: 0.8340 (pp20) cc_final: 0.8132 (pp20) REVERT: F 53 GLU cc_start: 0.8259 (tt0) cc_final: 0.7741 (tm-30) REVERT: F 55 ASN cc_start: 0.6622 (OUTLIER) cc_final: 0.5907 (p0) REVERT: K 5 LYS cc_start: 0.8892 (pptt) cc_final: 0.8573 (pptt) REVERT: K 86 LYS cc_start: 0.8706 (mtmt) cc_final: 0.8419 (mtmt) REVERT: L 1 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7816 (ttt) REVERT: L 9 ARG cc_start: 0.9165 (ttm-80) cc_final: 0.8947 (ttm-80) REVERT: L 27 LYS cc_start: 0.8714 (mttm) cc_final: 0.8342 (mtmm) REVERT: L 28 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8284 (mm-30) REVERT: L 31 GLU cc_start: 0.9455 (tp30) cc_final: 0.9236 (tp30) outliers start: 41 outliers final: 27 residues processed: 247 average time/residue: 0.3258 time to fit residues: 112.3877 Evaluate side-chains 233 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 202 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 55 ASN Chi-restraints excluded: chain K residue 22 ASP Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 85 GLN Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 50 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 115 optimal weight: 0.6980 chunk 63 optimal weight: 20.0000 chunk 131 optimal weight: 5.9990 chunk 106 optimal weight: 0.0570 chunk 0 optimal weight: 3.9990 chunk 78 optimal weight: 0.1980 chunk 138 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 overall best weight: 0.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 178 GLN L 32 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16255 Z= 0.204 Angle : 0.643 12.577 22918 Z= 0.352 Chirality : 0.039 0.225 2602 Planarity : 0.004 0.075 2209 Dihedral : 27.993 179.302 3937 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.81 % Allowed : 17.56 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.24 (0.22), residues: 1427 helix: 1.36 (0.19), residues: 719 sheet: -0.36 (0.34), residues: 211 loop : -1.36 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 160 HIS 0.011 0.001 HIS L 32 PHE 0.015 0.002 PHE C 215 TYR 0.020 0.002 TYR A 149 ARG 0.004 0.000 ARG K 36 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 228 time to evaluate : 1.573 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: A 53 MET cc_start: 0.8665 (mmt) cc_final: 0.8381 (mmm) REVERT: A 66 ARG cc_start: 0.7769 (ttt-90) cc_final: 0.7314 (mtm110) REVERT: A 110 ASP cc_start: 0.8682 (m-30) cc_final: 0.8313 (t0) REVERT: A 131 ARG cc_start: 0.8146 (mtt180) cc_final: 0.7544 (ptp-110) REVERT: A 155 GLN cc_start: 0.8342 (mt0) cc_final: 0.8092 (mt0) REVERT: A 164 ARG cc_start: 0.8982 (mtt180) cc_final: 0.8598 (ptp-110) REVERT: A 179 CYS cc_start: 0.8485 (m) cc_final: 0.7945 (p) REVERT: B 108 ASP cc_start: 0.7129 (t0) cc_final: 0.6911 (t0) REVERT: B 119 MET cc_start: 0.8287 (mtt) cc_final: 0.7153 (tmm) REVERT: B 154 LYS cc_start: 0.9114 (tttp) cc_final: 0.8890 (mmtm) REVERT: B 178 GLN cc_start: 0.7966 (mt0) cc_final: 0.7472 (mp10) REVERT: C 74 LEU cc_start: 0.8765 (tp) cc_final: 0.8371 (pp) REVERT: C 112 ARG cc_start: 0.7309 (ttt-90) cc_final: 0.7058 (ttm170) REVERT: C 177 ASN cc_start: 0.9390 (OUTLIER) cc_final: 0.8785 (t0) REVERT: C 191 THR cc_start: 0.8451 (m) cc_final: 0.8227 (p) REVERT: D 98 LYS cc_start: 0.8328 (mttt) cc_final: 0.8060 (mttp) REVERT: D 117 ARG cc_start: 0.8978 (mtp85) cc_final: 0.8731 (mmm-85) REVERT: D 264 LEU cc_start: 0.7335 (mt) cc_final: 0.6903 (mt) REVERT: E 9 GLU cc_start: 0.6316 (mt-10) cc_final: 0.6088 (mp0) REVERT: E 42 MET cc_start: 0.8825 (tmm) cc_final: 0.7940 (tmm) REVERT: E 45 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8013 (tm-30) REVERT: E 58 MET cc_start: 0.7702 (ttp) cc_final: 0.6823 (tmm) REVERT: F 42 MET cc_start: 0.8241 (tmm) cc_final: 0.7999 (ppp) REVERT: F 53 GLU cc_start: 0.8257 (tt0) cc_final: 0.7765 (tm-30) REVERT: F 55 ASN cc_start: 0.6393 (OUTLIER) cc_final: 0.5699 (p0) REVERT: K 5 LYS cc_start: 0.8856 (pptt) cc_final: 0.8640 (pptt) REVERT: K 86 LYS cc_start: 0.8647 (mtmt) cc_final: 0.8421 (mtmt) REVERT: L 28 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8229 (mm-30) REVERT: L 76 TYR cc_start: 0.7663 (m-80) cc_final: 0.6663 (t80) outliers start: 33 outliers final: 22 residues processed: 248 average time/residue: 0.3374 time to fit residues: 119.0011 Evaluate side-chains 227 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 203 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 55 ASN Chi-restraints excluded: chain K residue 22 ASP Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 85 GLN Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 50 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 0.5980 chunk 139 optimal weight: 10.0000 chunk 30 optimal weight: 0.4980 chunk 90 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 154 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 HIS C 70 GLN L 32 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 16255 Z= 0.376 Angle : 0.720 11.672 22918 Z= 0.390 Chirality : 0.041 0.150 2602 Planarity : 0.005 0.065 2209 Dihedral : 27.922 178.489 3937 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 21.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.41 % Allowed : 19.10 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.01 (0.22), residues: 1427 helix: 1.14 (0.18), residues: 719 sheet: -0.41 (0.34), residues: 215 loop : -1.49 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E 22 HIS 0.020 0.002 HIS L 32 PHE 0.023 0.002 PHE K 31 TYR 0.018 0.002 TYR C 149 ARG 0.006 0.001 ARG L 9 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 210 time to evaluate : 1.475 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: A 53 MET cc_start: 0.8705 (mmt) cc_final: 0.8459 (mmm) REVERT: A 66 ARG cc_start: 0.7829 (ttt-90) cc_final: 0.7366 (mtm110) REVERT: A 110 ASP cc_start: 0.8732 (m-30) cc_final: 0.8354 (t0) REVERT: A 131 ARG cc_start: 0.8381 (mtt180) cc_final: 0.7789 (mtm110) REVERT: A 155 GLN cc_start: 0.8296 (mt0) cc_final: 0.8050 (mt0) REVERT: A 179 CYS cc_start: 0.8528 (m) cc_final: 0.7953 (p) REVERT: B 108 ASP cc_start: 0.7118 (t0) cc_final: 0.6797 (t70) REVERT: B 119 MET cc_start: 0.8345 (mtt) cc_final: 0.7205 (tmm) REVERT: B 154 LYS cc_start: 0.9160 (tttp) cc_final: 0.8890 (mmtm) REVERT: C 74 LEU cc_start: 0.8826 (tp) cc_final: 0.8567 (tp) REVERT: C 112 ARG cc_start: 0.7498 (ttt-90) cc_final: 0.7162 (ttm170) REVERT: C 177 ASN cc_start: 0.9385 (OUTLIER) cc_final: 0.8822 (t0) REVERT: C 191 THR cc_start: 0.8560 (OUTLIER) cc_final: 0.8314 (p) REVERT: D 53 MET cc_start: 0.7847 (mpp) cc_final: 0.7570 (mpp) REVERT: D 98 LYS cc_start: 0.8372 (mttt) cc_final: 0.8097 (mttp) REVERT: D 120 PHE cc_start: 0.8486 (OUTLIER) cc_final: 0.7739 (m-80) REVERT: D 248 ARG cc_start: 0.5339 (mtt180) cc_final: 0.4924 (mtm110) REVERT: D 264 LEU cc_start: 0.7323 (mt) cc_final: 0.6847 (mt) REVERT: E 9 GLU cc_start: 0.6495 (mt-10) cc_final: 0.6221 (mp0) REVERT: E 42 MET cc_start: 0.8962 (tmm) cc_final: 0.8660 (tmm) REVERT: E 45 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8076 (tm-30) REVERT: F 53 GLU cc_start: 0.8349 (tt0) cc_final: 0.7742 (tm-30) REVERT: K 5 LYS cc_start: 0.8888 (pptt) cc_final: 0.8638 (pptt) REVERT: K 86 LYS cc_start: 0.8708 (mtmt) cc_final: 0.8462 (mtmt) REVERT: L 27 LYS cc_start: 0.8559 (mttm) cc_final: 0.8254 (mttm) REVERT: L 28 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8240 (mm-30) REVERT: L 33 MET cc_start: 0.8194 (mpp) cc_final: 0.7912 (mpp) REVERT: L 73 GLU cc_start: 0.9057 (mp0) cc_final: 0.8585 (pm20) REVERT: L 76 TYR cc_start: 0.7720 (m-80) cc_final: 0.6812 (t80) outliers start: 40 outliers final: 27 residues processed: 236 average time/residue: 0.3227 time to fit residues: 106.4232 Evaluate side-chains 224 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 194 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain K residue 22 ASP Chi-restraints excluded: chain K residue 33 GLU Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 85 GLN Chi-restraints excluded: chain L residue 50 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 5.9990 chunk 17 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 71 optimal weight: 0.0040 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16255 Z= 0.204 Angle : 0.645 9.554 22918 Z= 0.355 Chirality : 0.039 0.149 2602 Planarity : 0.005 0.082 2209 Dihedral : 27.859 178.650 3937 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.39 % Allowed : 20.38 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.39 (0.22), residues: 1427 helix: 1.50 (0.19), residues: 719 sheet: -0.35 (0.34), residues: 214 loop : -1.30 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP E 22 HIS 0.004 0.001 HIS L 32 PHE 0.016 0.002 PHE K 31 TYR 0.016 0.001 TYR C 149 ARG 0.008 0.000 ARG K 82 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 215 time to evaluate : 1.433 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: A 53 MET cc_start: 0.8695 (mmt) cc_final: 0.8389 (mmm) REVERT: A 66 ARG cc_start: 0.7763 (ttt-90) cc_final: 0.7300 (mtm110) REVERT: A 110 ASP cc_start: 0.8719 (m-30) cc_final: 0.8352 (t0) REVERT: A 131 ARG cc_start: 0.8260 (mtt180) cc_final: 0.7597 (mtm110) REVERT: A 155 GLN cc_start: 0.8351 (mt0) cc_final: 0.8143 (mt0) REVERT: A 164 ARG cc_start: 0.8906 (mtt-85) cc_final: 0.8353 (ttm110) REVERT: A 179 CYS cc_start: 0.8572 (m) cc_final: 0.7960 (p) REVERT: A 192 GLU cc_start: 0.6900 (tt0) cc_final: 0.6696 (tm-30) REVERT: B 108 ASP cc_start: 0.7019 (t0) cc_final: 0.6700 (t70) REVERT: B 119 MET cc_start: 0.8267 (mtt) cc_final: 0.7144 (tmm) REVERT: B 154 LYS cc_start: 0.9114 (tttp) cc_final: 0.8896 (mmtm) REVERT: C 74 LEU cc_start: 0.8774 (tp) cc_final: 0.8435 (pp) REVERT: C 112 ARG cc_start: 0.7309 (ttt-90) cc_final: 0.7018 (ttm170) REVERT: C 177 ASN cc_start: 0.9373 (OUTLIER) cc_final: 0.8803 (t0) REVERT: C 191 THR cc_start: 0.8317 (m) cc_final: 0.8105 (p) REVERT: D 264 LEU cc_start: 0.7241 (mt) cc_final: 0.6797 (mt) REVERT: E 9 GLU cc_start: 0.6374 (mt-10) cc_final: 0.6035 (mp0) REVERT: E 45 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8107 (tm-30) REVERT: E 58 MET cc_start: 0.7882 (ttp) cc_final: 0.7557 (tmm) REVERT: F 52 GLU cc_start: 0.8408 (pp20) cc_final: 0.8157 (pp20) REVERT: F 53 GLU cc_start: 0.8255 (tt0) cc_final: 0.7772 (tm-30) REVERT: F 55 ASN cc_start: 0.6379 (OUTLIER) cc_final: 0.5690 (p0) REVERT: K 86 LYS cc_start: 0.8658 (mtmt) cc_final: 0.8392 (mtmt) REVERT: L 14 GLN cc_start: 0.8524 (mm110) cc_final: 0.8142 (pp30) REVERT: L 27 LYS cc_start: 0.8506 (mttm) cc_final: 0.8231 (mttt) REVERT: L 28 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8294 (mm-30) REVERT: L 73 GLU cc_start: 0.9029 (mp0) cc_final: 0.8582 (pm20) REVERT: L 76 TYR cc_start: 0.7806 (m-80) cc_final: 0.6925 (t80) outliers start: 28 outliers final: 21 residues processed: 233 average time/residue: 0.3155 time to fit residues: 103.0584 Evaluate side-chains 222 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 199 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 55 ASN Chi-restraints excluded: chain K residue 22 ASP Chi-restraints excluded: chain K residue 33 GLU Chi-restraints excluded: chain L residue 32 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 30 optimal weight: 0.2980 chunk 29 optimal weight: 0.8980 chunk 98 optimal weight: 0.0980 chunk 105 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 14 optimal weight: 0.4980 chunk 121 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16255 Z= 0.194 Angle : 0.656 12.903 22918 Z= 0.355 Chirality : 0.039 0.192 2602 Planarity : 0.004 0.040 2209 Dihedral : 27.783 179.856 3937 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.47 % Allowed : 20.55 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.22), residues: 1427 helix: 1.59 (0.19), residues: 718 sheet: -0.25 (0.35), residues: 207 loop : -1.20 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 22 HIS 0.019 0.001 HIS L 32 PHE 0.014 0.002 PHE C 19 TYR 0.016 0.001 TYR C 101 ARG 0.005 0.000 ARG L 9 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 213 time to evaluate : 1.359 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: A 53 MET cc_start: 0.8688 (mmt) cc_final: 0.8153 (mmm) REVERT: A 110 ASP cc_start: 0.8715 (m-30) cc_final: 0.8344 (t0) REVERT: A 131 ARG cc_start: 0.8238 (mtt180) cc_final: 0.7598 (mtm110) REVERT: A 155 GLN cc_start: 0.8333 (mt0) cc_final: 0.8115 (mt0) REVERT: A 164 ARG cc_start: 0.8896 (mtt-85) cc_final: 0.8376 (ttm110) REVERT: A 179 CYS cc_start: 0.8579 (m) cc_final: 0.8056 (p) REVERT: A 192 GLU cc_start: 0.6883 (tt0) cc_final: 0.6668 (tm-30) REVERT: B 108 ASP cc_start: 0.6969 (t0) cc_final: 0.6685 (t70) REVERT: B 119 MET cc_start: 0.8271 (mtt) cc_final: 0.7156 (tmm) REVERT: B 154 LYS cc_start: 0.9122 (tttp) cc_final: 0.8908 (mmtm) REVERT: C 74 LEU cc_start: 0.8815 (tp) cc_final: 0.8601 (tp) REVERT: C 112 ARG cc_start: 0.7366 (ttt-90) cc_final: 0.7087 (ttm170) REVERT: C 177 ASN cc_start: 0.9414 (OUTLIER) cc_final: 0.8809 (t0) REVERT: D 264 LEU cc_start: 0.7232 (mt) cc_final: 0.6776 (mt) REVERT: E 9 GLU cc_start: 0.6414 (mt-10) cc_final: 0.6121 (mp0) REVERT: E 45 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8095 (tm-30) REVERT: F 9 GLU cc_start: 0.4946 (tt0) cc_final: 0.4651 (mm-30) REVERT: F 52 GLU cc_start: 0.8440 (pp20) cc_final: 0.8218 (pp20) REVERT: F 53 GLU cc_start: 0.8211 (tt0) cc_final: 0.7694 (tm-30) REVERT: F 55 ASN cc_start: 0.6629 (OUTLIER) cc_final: 0.6007 (p0) REVERT: K 90 ARG cc_start: 0.7738 (mtp180) cc_final: 0.7451 (ptm160) REVERT: L 14 GLN cc_start: 0.8502 (mm110) cc_final: 0.8100 (pp30) REVERT: L 27 LYS cc_start: 0.8442 (mttm) cc_final: 0.8182 (mttt) REVERT: L 28 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8287 (mm-30) REVERT: L 31 GLU cc_start: 0.9477 (tp30) cc_final: 0.9241 (tp30) REVERT: L 73 GLU cc_start: 0.9052 (mp0) cc_final: 0.8656 (pm20) outliers start: 29 outliers final: 18 residues processed: 233 average time/residue: 0.3095 time to fit residues: 102.3139 Evaluate side-chains 217 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 197 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 55 ASN Chi-restraints excluded: chain K residue 22 ASP Chi-restraints excluded: chain K residue 80 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 8.9990 chunk 147 optimal weight: 0.9980 chunk 134 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 129 optimal weight: 10.0000 chunk 135 optimal weight: 7.9990 chunk 94 optimal weight: 0.0070 overall best weight: 2.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 16255 Z= 0.348 Angle : 0.734 12.820 22918 Z= 0.391 Chirality : 0.041 0.217 2602 Planarity : 0.005 0.039 2209 Dihedral : 27.737 179.116 3937 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 20.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.90 % Allowed : 20.12 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.26 (0.22), residues: 1427 helix: 1.37 (0.19), residues: 719 sheet: -0.29 (0.34), residues: 228 loop : -1.41 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 22 HIS 0.007 0.001 HIS B 43 PHE 0.022 0.002 PHE C 19 TYR 0.021 0.002 TYR L 76 ARG 0.014 0.001 ARG D 248 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 202 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ASP cc_start: 0.8738 (m-30) cc_final: 0.8362 (t0) REVERT: A 131 ARG cc_start: 0.8388 (mtt180) cc_final: 0.7752 (mtm110) REVERT: A 155 GLN cc_start: 0.8307 (mt0) cc_final: 0.7994 (mt0) REVERT: A 164 ARG cc_start: 0.8984 (mtt-85) cc_final: 0.8558 (mtt-85) REVERT: A 179 CYS cc_start: 0.8494 (m) cc_final: 0.7931 (p) REVERT: B 108 ASP cc_start: 0.6905 (t0) cc_final: 0.6586 (t70) REVERT: B 119 MET cc_start: 0.8327 (mtt) cc_final: 0.7195 (tmm) REVERT: B 154 LYS cc_start: 0.9094 (tttp) cc_final: 0.8887 (mmtm) REVERT: C 53 MET cc_start: 0.8733 (mmp) cc_final: 0.8027 (mtt) REVERT: C 74 LEU cc_start: 0.8724 (tp) cc_final: 0.8390 (pp) REVERT: C 177 ASN cc_start: 0.9404 (OUTLIER) cc_final: 0.8843 (t0) REVERT: D 17 MET cc_start: 0.6824 (ptm) cc_final: 0.6434 (ptm) REVERT: D 264 LEU cc_start: 0.7245 (mt) cc_final: 0.6787 (mt) REVERT: E 9 GLU cc_start: 0.6502 (mt-10) cc_final: 0.6211 (mp0) REVERT: E 45 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8076 (tm-30) REVERT: F 53 GLU cc_start: 0.8336 (tt0) cc_final: 0.7722 (tm-30) REVERT: F 55 ASN cc_start: 0.6685 (OUTLIER) cc_final: 0.5979 (p0) REVERT: L 27 LYS cc_start: 0.8441 (mttm) cc_final: 0.8179 (mttt) REVERT: L 31 GLU cc_start: 0.9483 (tp30) cc_final: 0.9255 (tp30) outliers start: 34 outliers final: 24 residues processed: 228 average time/residue: 0.2929 time to fit residues: 95.9245 Evaluate side-chains 220 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 194 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 55 ASN Chi-restraints excluded: chain K residue 22 ASP Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 50 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 0.9980 chunk 92 optimal weight: 30.0000 chunk 72 optimal weight: 9.9990 chunk 105 optimal weight: 0.6980 chunk 159 optimal weight: 2.9990 chunk 146 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 98 optimal weight: 0.0470 chunk 77 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 71 GLN L 32 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16255 Z= 0.215 Angle : 0.690 12.926 22918 Z= 0.370 Chirality : 0.040 0.198 2602 Planarity : 0.004 0.038 2209 Dihedral : 27.700 178.464 3937 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.05 % Allowed : 21.14 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.22), residues: 1427 helix: 1.61 (0.19), residues: 719 sheet: -0.37 (0.34), residues: 219 loop : -1.18 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 22 HIS 0.010 0.001 HIS L 32 PHE 0.031 0.002 PHE D 19 TYR 0.014 0.001 TYR L 76 ARG 0.010 0.000 ARG D 248 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 200 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.8770 (mmp) cc_final: 0.7858 (mmm) REVERT: A 110 ASP cc_start: 0.8713 (m-30) cc_final: 0.8346 (t0) REVERT: A 131 ARG cc_start: 0.8295 (mtt180) cc_final: 0.7724 (mtm110) REVERT: A 155 GLN cc_start: 0.8372 (mt0) cc_final: 0.8150 (mt0) REVERT: A 164 ARG cc_start: 0.8912 (mtt-85) cc_final: 0.8388 (ttm110) REVERT: A 179 CYS cc_start: 0.8503 (m) cc_final: 0.7933 (p) REVERT: A 192 GLU cc_start: 0.6903 (tt0) cc_final: 0.6698 (tm-30) REVERT: B 108 ASP cc_start: 0.7017 (t0) cc_final: 0.6710 (t70) REVERT: B 119 MET cc_start: 0.8277 (mtt) cc_final: 0.7155 (tmm) REVERT: C 74 LEU cc_start: 0.8741 (tp) cc_final: 0.8389 (pp) REVERT: C 177 ASN cc_start: 0.9409 (OUTLIER) cc_final: 0.8851 (t0) REVERT: D 76 VAL cc_start: 0.8683 (OUTLIER) cc_final: 0.8346 (p) REVERT: D 264 LEU cc_start: 0.7234 (mt) cc_final: 0.6754 (mt) REVERT: E 9 GLU cc_start: 0.6527 (mt-10) cc_final: 0.6041 (mp0) REVERT: E 45 GLU cc_start: 0.8595 (mm-30) cc_final: 0.7998 (tm-30) REVERT: F 9 GLU cc_start: 0.4936 (tt0) cc_final: 0.4628 (mm-30) REVERT: F 52 GLU cc_start: 0.8465 (pp20) cc_final: 0.8247 (pp20) REVERT: F 53 GLU cc_start: 0.8270 (tt0) cc_final: 0.7751 (tm-30) REVERT: F 55 ASN cc_start: 0.6546 (OUTLIER) cc_final: 0.5983 (p0) REVERT: K 92 GLU cc_start: 0.6413 (pp20) cc_final: 0.5844 (pp20) REVERT: L 14 GLN cc_start: 0.8561 (mm110) cc_final: 0.8137 (pp30) outliers start: 24 outliers final: 18 residues processed: 219 average time/residue: 0.2942 time to fit residues: 93.5050 Evaluate side-chains 213 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 192 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 55 ASN Chi-restraints excluded: chain K residue 22 ASP Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain L residue 32 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.119758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.091587 restraints weight = 53390.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.092493 restraints weight = 28353.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.093152 restraints weight = 19193.798| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16255 Z= 0.292 Angle : 0.712 10.965 22918 Z= 0.383 Chirality : 0.041 0.208 2602 Planarity : 0.004 0.040 2209 Dihedral : 27.657 179.784 3937 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 19.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.30 % Allowed : 21.48 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.48 (0.22), residues: 1427 helix: 1.51 (0.19), residues: 719 sheet: -0.25 (0.34), residues: 217 loop : -1.18 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 22 HIS 0.021 0.002 HIS L 32 PHE 0.020 0.002 PHE D 32 TYR 0.014 0.002 TYR L 76 ARG 0.010 0.001 ARG D 248 =============================================================================== Job complete usr+sys time: 3230.51 seconds wall clock time: 59 minutes 15.85 seconds (3555.85 seconds total)