Starting phenix.real_space_refine on Sun Apr 7 17:04:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7y_36053/04_2024/8j7y_36053.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7y_36053/04_2024/8j7y_36053.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7y_36053/04_2024/8j7y_36053.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7y_36053/04_2024/8j7y_36053.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7y_36053/04_2024/8j7y_36053.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7y_36053/04_2024/8j7y_36053.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.055 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 Zn 2 6.06 5 S 46 5.16 5 C 7044 2.51 5 N 1830 2.21 5 O 2086 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 323": "OE1" <-> "OE2" Residue "A ASP 372": "OD1" <-> "OD2" Residue "E GLU 6": "OE1" <-> "OE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E ASP 72": "OD1" <-> "OD2" Residue "E ASP 88": "OD1" <-> "OD2" Residue "E GLU 102": "OE1" <-> "OE2" Residue "E GLU 153": "OE1" <-> "OE2" Residue "C GLU 27": "OE1" <-> "OE2" Residue "C TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 98": "OD1" <-> "OD2" Residue "C GLU 127": "OE1" <-> "OE2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 6": "OE1" <-> "OE2" Residue "F GLU 46": "OE1" <-> "OE2" Residue "F ASP 72": "OD1" <-> "OD2" Residue "F ASP 88": "OD1" <-> "OD2" Residue "F GLU 102": "OE1" <-> "OE2" Residue "F GLU 153": "OE1" <-> "OE2" Residue "B PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 323": "OE1" <-> "OE2" Residue "B ASP 372": "OD1" <-> "OD2" Residue "D GLU 27": "OE1" <-> "OE2" Residue "D TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 98": "OD1" <-> "OD2" Residue "D GLU 127": "OE1" <-> "OE2" Residue "D GLU 158": "OE1" <-> "OE2" Residue "D TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 11008 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2193 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 9, 'TRANS': 270} Chain breaks: 3 Chain: "E" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1638 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1672 Classifications: {'peptide': 215} Link IDs: {'PCIS': 4, 'PTRANS': 7, 'TRANS': 203} Chain: "F" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1638 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2193 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 9, 'TRANS': 270} Chain breaks: 3 Chain: "D" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1672 Classifications: {'peptide': 215} Link IDs: {'PCIS': 4, 'PTRANS': 7, 'TRANS': 203} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.99, per 1000 atoms: 0.54 Number of scatterers: 11008 At special positions: 0 Unit cell: (76.7, 116.82, 159.3, 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) Zn 2 29.99 S 46 16.00 O 2086 8.00 N 1830 7.00 C 7044 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 145 " - pdb=" SG CYS E 200 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 145 " - pdb=" SG CYS F 200 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 198 " distance=2.03 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: 4.33 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 240 " pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 240 " 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2668 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 26 sheets defined 31.3% alpha, 36.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 23 through 32 removed outlier: 3.986A pdb=" N ARG A 27 " --> pdb=" O SER A 23 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP A 32 " --> pdb=" O SER A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 57 Processing helix chain 'A' and resid 61 through 88 removed outlier: 4.222A pdb=" N SER A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 132 Processing helix chain 'A' and resid 143 through 159 Processing helix chain 'A' and resid 232 through 259 Processing helix chain 'A' and resid 267 through 294 Proline residue: A 284 - end of helix Processing helix chain 'A' and resid 303 through 314 removed outlier: 4.475A pdb=" N GLN A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 362 Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.527A pdb=" N ALA C 87 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 132 Processing helix chain 'C' and resid 187 through 192 Processing helix chain 'F' and resid 86 through 90 Processing helix chain 'F' and resid 161 through 163 No H-bonds generated for 'chain 'F' and resid 161 through 163' Processing helix chain 'B' and resid 23 through 32 removed outlier: 3.986A pdb=" N ARG B 27 " --> pdb=" O SER B 23 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP B 32 " --> pdb=" O SER B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 57 Processing helix chain 'B' and resid 61 through 88 removed outlier: 4.222A pdb=" N SER B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 132 Processing helix chain 'B' and resid 143 through 159 Processing helix chain 'B' and resid 232 through 259 Processing helix chain 'B' and resid 267 through 294 Proline residue: B 284 - end of helix Processing helix chain 'B' and resid 303 through 314 removed outlier: 4.475A pdb=" N GLN B 307 " --> pdb=" O ASN B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 362 Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.527A pdb=" N ALA D 87 " --> pdb=" O ALA D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 132 Processing helix chain 'D' and resid 187 through 192 Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 328 removed outlier: 5.558A pdb=" N LEU A 321 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE A 341 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N GLU A 323 " --> pdb=" O LYS A 339 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS A 339 " --> pdb=" O GLU A 323 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN A 366 " --> pdb=" O TYR A 334 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.666A pdb=" N THR E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.510A pdb=" N THR E 112 " --> pdb=" O TYR E 93 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR E 93 " --> pdb=" O THR E 112 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER E 40 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY E 44 " --> pdb=" O SER E 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.510A pdb=" N THR E 112 " --> pdb=" O TYR E 93 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR E 93 " --> pdb=" O THR E 112 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR E 107 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 125 through 129 removed outlier: 3.861A pdb=" N GLY E 144 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER E 184 " --> pdb=" O CYS E 145 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR E 180 " --> pdb=" O GLY E 149 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 125 through 129 removed outlier: 3.861A pdb=" N GLY E 144 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER E 184 " --> pdb=" O CYS E 145 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR E 180 " --> pdb=" O GLY E 149 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 156 through 159 removed outlier: 3.856A pdb=" N CYS E 200 " --> pdb=" O LYS E 213 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS E 213 " --> pdb=" O CYS E 200 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 14 removed outlier: 6.512A pdb=" N LEU C 11 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LYS C 111 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL C 13 " --> pdb=" O LYS C 111 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N MET C 37 " --> pdb=" O TYR C 53 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N TYR C 53 " --> pdb=" O MET C 37 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N TRP C 39 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 10 through 14 removed outlier: 6.512A pdb=" N LEU C 11 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LYS C 111 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL C 13 " --> pdb=" O LYS C 111 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR C 101 " --> pdb=" O GLN C 94 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AB3, first strand: chain 'C' and resid 118 through 122 removed outlier: 3.818A pdb=" N ASN C 141 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL C 137 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N TYR C 177 " --> pdb=" O ASN C 142 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 157 through 159 removed outlier: 4.659A pdb=" N TRP C 152 " --> pdb=" O ARG C 159 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N HIS C 202 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N SER C 207 " --> pdb=" O HIS C 202 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.666A pdb=" N THR F 21 " --> pdb=" O SER F 7 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.510A pdb=" N THR F 112 " --> pdb=" O TYR F 93 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR F 93 " --> pdb=" O THR F 112 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL F 34 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL F 50 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER F 40 " --> pdb=" O GLY F 44 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY F 44 " --> pdb=" O SER F 40 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.510A pdb=" N THR F 112 " --> pdb=" O TYR F 93 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR F 93 " --> pdb=" O THR F 112 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR F 107 " --> pdb=" O ARG F 97 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 125 through 129 removed outlier: 3.862A pdb=" N GLY F 144 " --> pdb=" O LEU F 129 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER F 184 " --> pdb=" O CYS F 145 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR F 180 " --> pdb=" O GLY F 149 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 125 through 129 removed outlier: 3.862A pdb=" N GLY F 144 " --> pdb=" O LEU F 129 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER F 184 " --> pdb=" O CYS F 145 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR F 180 " --> pdb=" O GLY F 149 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 156 through 159 removed outlier: 3.856A pdb=" N CYS F 200 " --> pdb=" O LYS F 213 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS F 213 " --> pdb=" O CYS F 200 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 318 through 328 removed outlier: 5.558A pdb=" N LEU B 321 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE B 341 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N GLU B 323 " --> pdb=" O LYS B 339 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS B 339 " --> pdb=" O GLU B 323 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN B 366 " --> pdb=" O TYR B 334 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'D' and resid 10 through 14 removed outlier: 6.512A pdb=" N LEU D 11 " --> pdb=" O GLU D 109 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LYS D 111 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL D 13 " --> pdb=" O LYS D 111 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N MET D 37 " --> pdb=" O TYR D 53 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N TYR D 53 " --> pdb=" O MET D 37 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TRP D 39 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 10 through 14 removed outlier: 6.512A pdb=" N LEU D 11 " --> pdb=" O GLU D 109 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LYS D 111 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL D 13 " --> pdb=" O LYS D 111 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR D 101 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 30 through 31 Processing sheet with id=AC7, first strand: chain 'D' and resid 118 through 122 removed outlier: 3.819A pdb=" N ASN D 141 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL D 137 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N TYR D 177 " --> pdb=" O ASN D 142 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 157 through 159 removed outlier: 4.660A pdb=" N TRP D 152 " --> pdb=" O ARG D 159 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N HIS D 202 " --> pdb=" O SER D 207 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N SER D 207 " --> pdb=" O HIS D 202 " (cutoff:3.500A) 620 hydrogen bonds defined for protein. 1716 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.67 Time building geometry restraints manager: 4.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3484 1.34 - 1.46: 2685 1.46 - 1.58: 5033 1.58 - 1.70: 0 1.70 - 1.81: 66 Bond restraints: 11268 Sorted by residual: bond pdb=" CG PRO C 145 " pdb=" CD PRO C 145 " ideal model delta sigma weight residual 1.512 1.486 0.026 2.70e-02 1.37e+03 9.13e-01 bond pdb=" C ASP A 267 " pdb=" N PRO A 268 " ideal model delta sigma weight residual 1.335 1.346 -0.012 1.28e-02 6.10e+03 8.51e-01 bond pdb=" CG PRO D 145 " pdb=" CD PRO D 145 " ideal model delta sigma weight residual 1.512 1.487 0.025 2.70e-02 1.37e+03 8.42e-01 bond pdb=" C ASP B 267 " pdb=" N PRO B 268 " ideal model delta sigma weight residual 1.335 1.346 -0.012 1.28e-02 6.10e+03 8.18e-01 bond pdb=" CG PRO C 99 " pdb=" CD PRO C 99 " ideal model delta sigma weight residual 1.512 1.489 0.023 2.70e-02 1.37e+03 7.08e-01 ... (remaining 11263 not shown) Histogram of bond angle deviations from ideal: 98.81 - 105.85: 260 105.85 - 112.89: 6159 112.89 - 119.92: 3523 119.92 - 126.96: 5247 126.96 - 134.00: 153 Bond angle restraints: 15342 Sorted by residual: angle pdb=" C VAL E 188 " pdb=" CA VAL E 188 " pdb=" CB VAL E 188 " ideal model delta sigma weight residual 109.33 112.33 -3.00 9.80e-01 1.04e+00 9.39e+00 angle pdb=" C VAL F 188 " pdb=" CA VAL F 188 " pdb=" CB VAL F 188 " ideal model delta sigma weight residual 109.33 112.33 -3.00 9.80e-01 1.04e+00 9.37e+00 angle pdb=" CA VAL F 188 " pdb=" C VAL F 188 " pdb=" N PRO F 189 " ideal model delta sigma weight residual 116.57 119.43 -2.86 9.80e-01 1.04e+00 8.55e+00 angle pdb=" CA VAL E 188 " pdb=" C VAL E 188 " pdb=" N PRO E 189 " ideal model delta sigma weight residual 116.57 119.40 -2.83 9.80e-01 1.04e+00 8.37e+00 angle pdb=" CA LYS C 153 " pdb=" CB LYS C 153 " pdb=" CG LYS C 153 " ideal model delta sigma weight residual 114.10 119.54 -5.44 2.00e+00 2.50e-01 7.40e+00 ... (remaining 15337 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 6097 17.88 - 35.77: 463 35.77 - 53.65: 72 53.65 - 71.54: 20 71.54 - 89.42: 8 Dihedral angle restraints: 6660 sinusoidal: 2526 harmonic: 4134 Sorted by residual: dihedral pdb=" CB CYS F 145 " pdb=" SG CYS F 145 " pdb=" SG CYS F 200 " pdb=" CB CYS F 200 " ideal model delta sinusoidal sigma weight residual 93.00 149.76 -56.76 1 1.00e+01 1.00e-02 4.34e+01 dihedral pdb=" CB CYS E 145 " pdb=" SG CYS E 145 " pdb=" SG CYS E 200 " pdb=" CB CYS E 200 " ideal model delta sinusoidal sigma weight residual 93.00 149.73 -56.73 1 1.00e+01 1.00e-02 4.33e+01 dihedral pdb=" CB CYS D 23 " pdb=" SG CYS D 23 " pdb=" SG CYS D 92 " pdb=" CB CYS D 92 " ideal model delta sinusoidal sigma weight residual 93.00 57.45 35.55 1 1.00e+01 1.00e-02 1.79e+01 ... (remaining 6657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1107 0.029 - 0.057: 406 0.057 - 0.086: 144 0.086 - 0.115: 94 0.115 - 0.144: 15 Chirality restraints: 1766 Sorted by residual: chirality pdb=" CA ILE E 92 " pdb=" N ILE E 92 " pdb=" C ILE E 92 " pdb=" CB ILE E 92 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" CA ILE F 92 " pdb=" N ILE F 92 " pdb=" C ILE F 92 " pdb=" CB ILE F 92 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA ASN B 152 " pdb=" N ASN B 152 " pdb=" C ASN B 152 " pdb=" CB ASN B 152 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 1763 not shown) Planarity restraints: 1938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU F 153 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO F 154 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO F 154 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO F 154 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU E 153 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO E 154 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO E 154 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 154 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 188 " -0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO F 189 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO F 189 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 189 " -0.023 5.00e-02 4.00e+02 ... (remaining 1935 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 62 2.51 - 3.11: 8088 3.11 - 3.71: 16902 3.71 - 4.30: 23705 4.30 - 4.90: 40316 Nonbonded interactions: 89073 Sorted by model distance: nonbonded pdb=" CG ASP A 74 " pdb="ZN ZN A 501 " model vdw 1.914 2.460 nonbonded pdb=" CG ASP B 74 " pdb="ZN ZN B 501 " model vdw 1.914 2.460 nonbonded pdb=" OD1 ASP A 74 " pdb="ZN ZN A 501 " model vdw 2.008 2.230 nonbonded pdb=" OD1 ASP B 74 " pdb="ZN ZN B 501 " model vdw 2.009 2.230 nonbonded pdb=" OD2 ASP B 244 " pdb="ZN ZN B 501 " model vdw 2.063 2.230 ... (remaining 89068 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' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 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: 5.360 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 33.990 Find NCS groups from input model: 0.600 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: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 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 : 0.002 0.037 11268 Z= 0.127 Angle : 0.505 7.010 15342 Z= 0.261 Chirality : 0.040 0.144 1766 Planarity : 0.003 0.050 1938 Dihedral : 13.140 89.420 3968 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.16 % Allowed : 0.33 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % 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: 1.40 (0.23), residues: 1402 helix: 2.44 (0.25), residues: 422 sheet: 0.89 (0.25), residues: 470 loop : -0.29 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 152 HIS 0.009 0.001 HIS A 240 PHE 0.005 0.001 PHE C 102 TYR 0.017 0.001 TYR E 101 ARG 0.001 0.000 ARG E 97 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 322 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8169 (pp20) cc_final: 0.7904 (pp20) REVERT: A 128 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7634 (mt-10) REVERT: A 319 TYR cc_start: 0.7798 (m-80) cc_final: 0.7569 (m-80) REVERT: C 4 LEU cc_start: 0.8703 (mt) cc_final: 0.8475 (mt) REVERT: C 78 THR cc_start: 0.8820 (m) cc_final: 0.8502 (p) REVERT: C 79 ILE cc_start: 0.8362 (mt) cc_final: 0.8128 (mt) REVERT: C 151 LYS cc_start: 0.8139 (mtpp) cc_final: 0.7564 (mmmt) REVERT: B 33 LYS cc_start: 0.9496 (pptt) cc_final: 0.9287 (tppt) REVERT: B 37 ASN cc_start: 0.9189 (m110) cc_final: 0.8798 (m-40) REVERT: B 50 PHE cc_start: 0.8885 (m-10) cc_final: 0.8529 (m-10) REVERT: B 73 PHE cc_start: 0.6674 (m-10) cc_final: 0.6469 (m-10) REVERT: B 120 PHE cc_start: 0.8059 (m-10) cc_final: 0.7826 (m-10) REVERT: B 154 ILE cc_start: 0.8674 (mm) cc_final: 0.8401 (mm) REVERT: B 257 MET cc_start: 0.5897 (tmm) cc_final: 0.5556 (ptm) REVERT: D 107 LYS cc_start: 0.8171 (mtpp) cc_final: 0.7971 (mmmt) REVERT: D 151 LYS cc_start: 0.8290 (mtpp) cc_final: 0.8080 (mmmt) REVERT: D 179 MET cc_start: 0.8227 (ttp) cc_final: 0.7978 (ttp) outliers start: 2 outliers final: 0 residues processed: 322 average time/residue: 0.2122 time to fit residues: 98.2933 Evaluate side-chains 197 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 109 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS A 295 GLN A 361 GLN C 165 ASN F 73 ASN D 160 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11268 Z= 0.263 Angle : 0.622 11.074 15342 Z= 0.324 Chirality : 0.045 0.168 1766 Planarity : 0.004 0.055 1938 Dihedral : 3.888 15.775 1520 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.47 % Allowed : 11.56 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % 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: 1.22 (0.23), residues: 1402 helix: 2.31 (0.25), residues: 424 sheet: 0.85 (0.24), residues: 464 loop : -0.48 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 152 HIS 0.003 0.001 HIS A 240 PHE 0.019 0.002 PHE B 359 TYR 0.015 0.002 TYR E 150 ARG 0.004 0.000 ARG F 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 210 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ASP cc_start: 0.8645 (t0) cc_final: 0.8207 (t0) REVERT: A 37 ASN cc_start: 0.9272 (m110) cc_final: 0.9036 (p0) REVERT: A 52 GLU cc_start: 0.8174 (pp20) cc_final: 0.7869 (pp20) REVERT: A 74 ASP cc_start: 0.6724 (m-30) cc_final: 0.6511 (m-30) REVERT: A 128 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7651 (mt-10) REVERT: A 240 HIS cc_start: 0.7390 (t-90) cc_final: 0.7000 (t-90) REVERT: E 72 ASP cc_start: 0.7392 (t0) cc_final: 0.7167 (t0) REVERT: E 176 GLN cc_start: 0.7504 (tm-30) cc_final: 0.7269 (tm-30) REVERT: C 37 MET cc_start: 0.7777 (tpp) cc_final: 0.7531 (tpp) REVERT: C 160 GLN cc_start: 0.8085 (mp10) cc_final: 0.7601 (mp10) REVERT: F 32 TYR cc_start: 0.8547 (m-80) cc_final: 0.8197 (m-80) REVERT: F 72 ASP cc_start: 0.7682 (t0) cc_final: 0.6855 (t0) REVERT: B 50 PHE cc_start: 0.8874 (m-10) cc_final: 0.8498 (m-10) REVERT: B 154 ILE cc_start: 0.8723 (mm) cc_final: 0.8460 (mm) REVERT: D 149 ASN cc_start: 0.8686 (m-40) cc_final: 0.8447 (m-40) REVERT: D 194 ASN cc_start: 0.8840 (t0) cc_final: 0.8633 (t0) outliers start: 18 outliers final: 10 residues processed: 221 average time/residue: 0.2111 time to fit residues: 68.1067 Evaluate side-chains 196 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 186 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain D residue 32 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 0.0670 chunk 105 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 43 optimal weight: 0.0870 chunk 102 optimal weight: 8.9990 overall best weight: 0.5896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 201 ASN B 70 HIS D 41 GLN D 160 GLN D 214 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11268 Z= 0.194 Angle : 0.551 12.146 15342 Z= 0.284 Chirality : 0.043 0.296 1766 Planarity : 0.004 0.051 1938 Dihedral : 3.678 14.791 1520 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.71 % Allowed : 12.87 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % 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: 1.25 (0.22), residues: 1402 helix: 2.34 (0.25), residues: 424 sheet: 0.79 (0.24), residues: 458 loop : -0.36 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 58 HIS 0.004 0.001 HIS B 240 PHE 0.052 0.001 PHE A 149 TYR 0.014 0.001 TYR C 190 ARG 0.002 0.000 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 196 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ASP cc_start: 0.8613 (t0) cc_final: 0.8160 (t0) REVERT: A 52 GLU cc_start: 0.8031 (pp20) cc_final: 0.7746 (pp20) REVERT: A 74 ASP cc_start: 0.6811 (m-30) cc_final: 0.6554 (m-30) REVERT: A 128 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7648 (mt-10) REVERT: A 240 HIS cc_start: 0.7753 (t-90) cc_final: 0.7127 (t-90) REVERT: A 288 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7201 (tm-30) REVERT: E 92 ILE cc_start: 0.9067 (mp) cc_final: 0.8842 (mt) REVERT: E 120 LYS cc_start: 0.8556 (mmmm) cc_final: 0.8310 (mmmm) REVERT: E 176 GLN cc_start: 0.7640 (tm-30) cc_final: 0.7298 (tm-30) REVERT: B 50 PHE cc_start: 0.8813 (m-10) cc_final: 0.8502 (m-10) REVERT: B 74 ASP cc_start: 0.6890 (m-30) cc_final: 0.6507 (m-30) REVERT: B 154 ILE cc_start: 0.8703 (mm) cc_final: 0.8460 (mm) REVERT: D 169 ASP cc_start: 0.8217 (m-30) cc_final: 0.8013 (m-30) outliers start: 21 outliers final: 16 residues processed: 210 average time/residue: 0.2005 time to fit residues: 62.2714 Evaluate side-chains 199 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 183 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 147 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 295 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11268 Z= 0.329 Angle : 0.599 9.101 15342 Z= 0.313 Chirality : 0.044 0.160 1766 Planarity : 0.004 0.053 1938 Dihedral : 3.841 14.610 1520 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.87 % Allowed : 14.33 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % 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: 1.12 (0.22), residues: 1402 helix: 2.28 (0.25), residues: 428 sheet: 0.65 (0.24), residues: 458 loop : -0.44 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 108 HIS 0.004 0.001 HIS A 240 PHE 0.016 0.001 PHE B 238 TYR 0.016 0.002 TYR E 150 ARG 0.003 0.000 ARG D 215 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 184 time to evaluate : 1.235 Fit side-chains revert: symmetry clash REVERT: A 32 ASP cc_start: 0.8531 (t0) cc_final: 0.7857 (t0) REVERT: A 52 GLU cc_start: 0.8112 (pp20) cc_final: 0.7864 (pp20) REVERT: A 128 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7733 (mt-10) REVERT: A 288 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7299 (tm-30) REVERT: E 176 GLN cc_start: 0.7843 (tm-30) cc_final: 0.7415 (tm-30) REVERT: F 181 THR cc_start: 0.9077 (OUTLIER) cc_final: 0.8877 (m) REVERT: B 50 PHE cc_start: 0.8858 (m-10) cc_final: 0.8538 (m-10) REVERT: B 154 ILE cc_start: 0.8659 (mm) cc_final: 0.8393 (mm) outliers start: 23 outliers final: 20 residues processed: 201 average time/residue: 0.2066 time to fit residues: 61.0398 Evaluate side-chains 199 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 178 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 141 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 0.0020 chunk 1 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 93 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 201 ASN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11268 Z= 0.204 Angle : 0.554 7.152 15342 Z= 0.287 Chirality : 0.042 0.154 1766 Planarity : 0.004 0.050 1938 Dihedral : 3.738 14.886 1520 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.55 % Allowed : 15.72 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % 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: 1.17 (0.22), residues: 1402 helix: 2.29 (0.25), residues: 428 sheet: 0.70 (0.24), residues: 458 loop : -0.40 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 159 HIS 0.003 0.001 HIS B 240 PHE 0.029 0.001 PHE B 238 TYR 0.024 0.001 TYR E 150 ARG 0.001 0.000 ARG D 159 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 185 time to evaluate : 1.373 Fit side-chains REVERT: A 32 ASP cc_start: 0.8531 (t0) cc_final: 0.8067 (t0) REVERT: A 52 GLU cc_start: 0.8110 (pp20) cc_final: 0.7835 (pp20) REVERT: A 128 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7732 (mt-10) REVERT: E 176 GLN cc_start: 0.7866 (tm-30) cc_final: 0.7430 (tm-30) REVERT: C 158 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7496 (tm-30) REVERT: C 160 GLN cc_start: 0.7851 (pm20) cc_final: 0.7603 (pm20) REVERT: B 50 PHE cc_start: 0.8851 (m-10) cc_final: 0.8524 (m-10) REVERT: B 154 ILE cc_start: 0.8709 (mm) cc_final: 0.8427 (mm) REVERT: B 288 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7813 (tm-30) REVERT: D 127 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7911 (mp0) outliers start: 19 outliers final: 9 residues processed: 201 average time/residue: 0.2073 time to fit residues: 61.4348 Evaluate side-chains 180 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 170 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain D residue 127 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 135 optimal weight: 0.6980 chunk 112 optimal weight: 0.0870 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 30.0000 chunk 44 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 HIS F 169 HIS F 201 ASN D 128 GLN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11268 Z= 0.193 Angle : 0.583 15.160 15342 Z= 0.296 Chirality : 0.042 0.168 1766 Planarity : 0.004 0.052 1938 Dihedral : 3.727 15.544 1520 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.63 % Allowed : 15.88 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % 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: 1.17 (0.23), residues: 1402 helix: 2.20 (0.25), residues: 428 sheet: 0.69 (0.24), residues: 464 loop : -0.33 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 159 HIS 0.002 0.001 HIS B 240 PHE 0.022 0.001 PHE B 114 TYR 0.026 0.001 TYR E 150 ARG 0.003 0.000 ARG C 65 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 183 time to evaluate : 1.251 Fit side-chains REVERT: A 32 ASP cc_start: 0.8498 (t0) cc_final: 0.8041 (t0) REVERT: A 52 GLU cc_start: 0.8108 (pp20) cc_final: 0.7860 (pp20) REVERT: A 128 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7853 (mt-10) REVERT: A 288 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7372 (tm-30) REVERT: E 176 GLN cc_start: 0.7871 (tm-30) cc_final: 0.7443 (tm-30) REVERT: B 37 ASN cc_start: 0.9273 (m110) cc_final: 0.8637 (m110) REVERT: B 50 PHE cc_start: 0.8855 (m-10) cc_final: 0.8529 (m-10) REVERT: B 154 ILE cc_start: 0.8817 (mm) cc_final: 0.8570 (mm) outliers start: 20 outliers final: 14 residues processed: 199 average time/residue: 0.2106 time to fit residues: 61.5325 Evaluate side-chains 192 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 178 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain D residue 141 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 10.0000 chunk 77 optimal weight: 0.4980 chunk 98 optimal weight: 2.9990 chunk 76 optimal weight: 0.1980 chunk 114 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN F 201 ASN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11268 Z= 0.217 Angle : 0.587 12.613 15342 Z= 0.299 Chirality : 0.042 0.153 1766 Planarity : 0.004 0.052 1938 Dihedral : 3.746 15.900 1520 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.63 % Allowed : 16.78 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % 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: 1.15 (0.23), residues: 1402 helix: 2.21 (0.25), residues: 428 sheet: 0.65 (0.24), residues: 464 loop : -0.32 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 159 HIS 0.002 0.001 HIS E 35 PHE 0.025 0.001 PHE B 114 TYR 0.028 0.001 TYR E 150 ARG 0.003 0.000 ARG C 65 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 184 time to evaluate : 1.316 Fit side-chains REVERT: A 32 ASP cc_start: 0.8467 (t0) cc_final: 0.7945 (t70) REVERT: A 52 GLU cc_start: 0.8147 (pp20) cc_final: 0.7888 (pp20) REVERT: A 74 ASP cc_start: 0.6781 (m-30) cc_final: 0.6493 (m-30) REVERT: A 128 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7854 (mt-10) REVERT: A 288 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7381 (tm-30) REVERT: E 176 GLN cc_start: 0.7924 (tm-30) cc_final: 0.7490 (tm-30) REVERT: C 109 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7182 (tt0) REVERT: C 127 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8411 (mp0) REVERT: B 50 PHE cc_start: 0.8845 (m-10) cc_final: 0.8533 (m-10) REVERT: B 71 MET cc_start: 0.8617 (ppp) cc_final: 0.8266 (ppp) REVERT: B 154 ILE cc_start: 0.8803 (mm) cc_final: 0.8566 (mm) outliers start: 20 outliers final: 16 residues processed: 199 average time/residue: 0.2133 time to fit residues: 62.5522 Evaluate side-chains 190 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 174 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain D residue 141 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 0.0870 chunk 85 optimal weight: 0.6980 chunk 91 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 106 optimal weight: 0.8980 chunk 122 optimal weight: 0.5980 chunk 129 optimal weight: 2.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 ASN C 214 ASN F 201 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11268 Z= 0.201 Angle : 0.600 12.505 15342 Z= 0.306 Chirality : 0.042 0.156 1766 Planarity : 0.004 0.052 1938 Dihedral : 3.734 23.423 1520 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.38 % Allowed : 17.35 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % 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: 1.18 (0.23), residues: 1402 helix: 2.20 (0.25), residues: 428 sheet: 0.69 (0.24), residues: 464 loop : -0.28 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 58 HIS 0.003 0.001 HIS B 161 PHE 0.021 0.001 PHE B 149 TYR 0.027 0.001 TYR E 150 ARG 0.006 0.000 ARG C 215 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 184 time to evaluate : 1.206 Fit side-chains REVERT: A 32 ASP cc_start: 0.8432 (t0) cc_final: 0.7929 (t70) REVERT: A 52 GLU cc_start: 0.8130 (pp20) cc_final: 0.7898 (pp20) REVERT: A 74 ASP cc_start: 0.6806 (m-30) cc_final: 0.6509 (m-30) REVERT: A 128 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7889 (mt-10) REVERT: A 288 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7374 (tm-30) REVERT: E 176 GLN cc_start: 0.7863 (tm-30) cc_final: 0.7442 (tm-30) REVERT: C 109 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7194 (tt0) REVERT: C 147 ASP cc_start: 0.7815 (t0) cc_final: 0.7571 (t0) REVERT: B 50 PHE cc_start: 0.8842 (m-10) cc_final: 0.8504 (m-10) REVERT: B 71 MET cc_start: 0.8592 (ppp) cc_final: 0.8363 (ppp) REVERT: B 154 ILE cc_start: 0.8813 (mm) cc_final: 0.8572 (mm) outliers start: 17 outliers final: 13 residues processed: 194 average time/residue: 0.2152 time to fit residues: 61.1301 Evaluate side-chains 193 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 180 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain B residue 305 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 129 optimal weight: 0.0040 chunk 75 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 38 optimal weight: 0.4980 chunk 113 optimal weight: 0.5980 chunk 118 optimal weight: 0.7980 chunk 82 optimal weight: 0.0670 chunk 132 optimal weight: 0.5980 overall best weight: 0.3530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11268 Z= 0.171 Angle : 0.606 18.679 15342 Z= 0.303 Chirality : 0.042 0.159 1766 Planarity : 0.004 0.052 1938 Dihedral : 3.642 16.379 1520 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.71 % Allowed : 17.35 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % 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: 1.22 (0.23), residues: 1402 helix: 2.21 (0.25), residues: 428 sheet: 0.73 (0.24), residues: 464 loop : -0.26 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 58 HIS 0.002 0.000 HIS B 161 PHE 0.022 0.001 PHE B 149 TYR 0.028 0.001 TYR E 150 ARG 0.002 0.000 ARG D 159 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 188 time to evaluate : 1.258 Fit side-chains REVERT: A 32 ASP cc_start: 0.8409 (t0) cc_final: 0.7747 (t0) REVERT: A 52 GLU cc_start: 0.8128 (pp20) cc_final: 0.7894 (pp20) REVERT: A 74 ASP cc_start: 0.6826 (m-30) cc_final: 0.6520 (m-30) REVERT: A 128 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7880 (mt-10) REVERT: A 288 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7360 (tm-30) REVERT: A 302 GLU cc_start: 0.7745 (tt0) cc_final: 0.7533 (tt0) REVERT: E 176 GLN cc_start: 0.7859 (tm-30) cc_final: 0.7446 (tm-30) REVERT: C 109 GLU cc_start: 0.7439 (mt-10) cc_final: 0.7211 (tt0) REVERT: B 50 PHE cc_start: 0.8797 (m-10) cc_final: 0.8453 (m-10) REVERT: B 94 ASP cc_start: 0.7791 (t0) cc_final: 0.7514 (t0) REVERT: B 154 ILE cc_start: 0.8759 (mm) cc_final: 0.8450 (mm) outliers start: 21 outliers final: 17 residues processed: 204 average time/residue: 0.2039 time to fit residues: 62.0725 Evaluate side-chains 195 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 178 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain D residue 141 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 11 optimal weight: 0.1980 chunk 85 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.5105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11268 Z= 0.215 Angle : 0.617 16.264 15342 Z= 0.311 Chirality : 0.042 0.156 1766 Planarity : 0.004 0.052 1938 Dihedral : 3.727 24.166 1520 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.30 % Allowed : 17.92 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % 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: 1.21 (0.23), residues: 1402 helix: 2.21 (0.25), residues: 428 sheet: 0.70 (0.24), residues: 464 loop : -0.26 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 58 HIS 0.002 0.001 HIS E 35 PHE 0.023 0.001 PHE B 149 TYR 0.030 0.001 TYR E 150 ARG 0.002 0.000 ARG C 159 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 184 time to evaluate : 1.086 Fit side-chains REVERT: A 32 ASP cc_start: 0.8448 (t0) cc_final: 0.7791 (t0) REVERT: A 52 GLU cc_start: 0.8114 (pp20) cc_final: 0.7874 (pp20) REVERT: A 128 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7883 (mt-10) REVERT: A 288 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7387 (tm-30) REVERT: E 176 GLN cc_start: 0.7898 (tm-30) cc_final: 0.7480 (tm-30) REVERT: C 109 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7324 (tt0) REVERT: B 50 PHE cc_start: 0.8791 (m-10) cc_final: 0.8447 (m-10) REVERT: B 154 ILE cc_start: 0.8760 (mm) cc_final: 0.8451 (mm) outliers start: 16 outliers final: 14 residues processed: 196 average time/residue: 0.1599 time to fit residues: 46.4738 Evaluate side-chains 198 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 184 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain D residue 141 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 20.0000 chunk 16 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 chunk 111 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 114 optimal weight: 0.0970 chunk 14 optimal weight: 5.9990 chunk 20 optimal weight: 0.0670 chunk 97 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.118691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.081124 restraints weight = 20134.020| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.45 r_work: 0.2990 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.5188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11268 Z= 0.194 Angle : 0.612 16.992 15342 Z= 0.307 Chirality : 0.042 0.157 1766 Planarity : 0.004 0.052 1938 Dihedral : 3.672 17.321 1520 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.38 % Allowed : 17.67 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % 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: 1.24 (0.23), residues: 1402 helix: 2.23 (0.25), residues: 428 sheet: 0.73 (0.24), residues: 464 loop : -0.25 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 58 HIS 0.002 0.001 HIS B 161 PHE 0.023 0.001 PHE B 149 TYR 0.029 0.001 TYR E 150 ARG 0.002 0.000 ARG C 159 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2603.40 seconds wall clock time: 50 minutes 33.60 seconds (3033.60 seconds total)