Starting phenix.real_space_refine on Sun Jul 21 13:46:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8i_6179/07_2024/3j8i_6179_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8i_6179/07_2024/3j8i_6179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8i_6179/07_2024/3j8i_6179.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8i_6179/07_2024/3j8i_6179.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8i_6179/07_2024/3j8i_6179_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8i_6179/07_2024/3j8i_6179_neut.cif" } resolution = 4.7 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= -0.009 sd= 0.016 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: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 105 5.16 5 C 9320 2.51 5 N 2490 2.21 5 O 2870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 4": "OE1" <-> "OE2" Residue "D ARG 62": "NH1" <-> "NH2" Residue "D GLU 72": "OE1" <-> "OE2" Residue "D ASP 81": "OD1" <-> "OD2" Residue "D GLU 99": "OE1" <-> "OE2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D GLU 205": "OE1" <-> "OE2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D GLU 237": "OE1" <-> "OE2" Residue "D TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 253": "OE1" <-> "OE2" Residue "D TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 334": "OE1" <-> "OE2" Residue "D ARG 335": "NH1" <-> "NH2" Residue "D TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 364": "OE1" <-> "OE2" Residue "D ARG 372": "NH1" <-> "NH2" Residue "D PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 4": "OE1" <-> "OE2" Residue "E ARG 62": "NH1" <-> "NH2" Residue "E GLU 72": "OE1" <-> "OE2" Residue "E ASP 81": "OD1" <-> "OD2" Residue "E GLU 99": "OE1" <-> "OE2" Residue "E GLU 100": "OE1" <-> "OE2" Residue "E GLU 205": "OE1" <-> "OE2" Residue "E GLU 224": "OE1" <-> "OE2" Residue "E GLU 237": "OE1" <-> "OE2" Residue "E TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 253": "OE1" <-> "OE2" Residue "E GLU 334": "OE1" <-> "OE2" Residue "E ARG 335": "NH1" <-> "NH2" Residue "E TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 364": "OE1" <-> "OE2" Residue "E ARG 372": "NH1" <-> "NH2" Residue "E PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 4": "OE1" <-> "OE2" Residue "F ARG 62": "NH1" <-> "NH2" Residue "F GLU 72": "OE1" <-> "OE2" Residue "F ASP 81": "OD1" <-> "OD2" Residue "F GLU 99": "OE1" <-> "OE2" Residue "F GLU 100": "OE1" <-> "OE2" Residue "F GLU 205": "OE1" <-> "OE2" Residue "F GLU 224": "OE1" <-> "OE2" Residue "F GLU 237": "OE1" <-> "OE2" Residue "F TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 253": "OE1" <-> "OE2" Residue "F TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 334": "OE1" <-> "OE2" Residue "F ARG 335": "NH1" <-> "NH2" Residue "F TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 364": "OE1" <-> "OE2" Residue "F ARG 372": "NH1" <-> "NH2" Residue "F PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 4": "OE1" <-> "OE2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "G GLU 72": "OE1" <-> "OE2" Residue "G ASP 81": "OD1" <-> "OD2" Residue "G GLU 99": "OE1" <-> "OE2" Residue "G GLU 100": "OE1" <-> "OE2" Residue "G GLU 205": "OE1" <-> "OE2" Residue "G GLU 224": "OE1" <-> "OE2" Residue "G GLU 237": "OE1" <-> "OE2" Residue "G TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 253": "OE1" <-> "OE2" Residue "G TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 334": "OE1" <-> "OE2" Residue "G ARG 335": "NH1" <-> "NH2" Residue "G TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 364": "OE1" <-> "OE2" Residue "G ARG 372": "NH1" <-> "NH2" Residue "G PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 4": "OE1" <-> "OE2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H GLU 72": "OE1" <-> "OE2" Residue "H ASP 81": "OD1" <-> "OD2" Residue "H GLU 99": "OE1" <-> "OE2" Residue "H GLU 100": "OE1" <-> "OE2" Residue "H GLU 205": "OE1" <-> "OE2" Residue "H GLU 224": "OE1" <-> "OE2" Residue "H GLU 237": "OE1" <-> "OE2" Residue "H TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 253": "OE1" <-> "OE2" Residue "H GLU 334": "OE1" <-> "OE2" Residue "H ARG 335": "NH1" <-> "NH2" Residue "H TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 364": "OE1" <-> "OE2" Residue "H ARG 372": "NH1" <-> "NH2" Residue "H PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 14800 Number of models: 1 Model: "" Number of chains: 10 Chain: "D" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2932 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "E" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2932 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "F" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2932 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "G" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2932 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "H" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2932 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.61, per 1000 atoms: 0.51 Number of scatterers: 14800 At special positions: 0 Unit cell: (110.25, 86.1, 194.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 105 16.00 P 10 15.00 Mg 5 11.99 O 2870 8.00 N 2490 7.00 C 9320 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: 5.71 Conformation dependent library (CDL) restraints added in 2.8 seconds 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3470 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 15 sheets defined 40.9% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'D' and resid 56 through 61 Processing helix chain 'D' and resid 82 through 91 removed outlier: 3.859A pdb=" N TRP D 86 " --> pdb=" O MET D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.049A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 144 removed outlier: 4.118A pdb=" N SER D 141 " --> pdb=" O GLN D 137 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 202 through 210 Processing helix chain 'D' and resid 211 through 216 Processing helix chain 'D' and resid 223 through 233 removed outlier: 3.595A pdb=" N ALA D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.979A pdb=" N ARG D 256 " --> pdb=" O ASN D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 263 removed outlier: 3.724A pdb=" N PHE D 262 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 284 removed outlier: 3.790A pdb=" N TYR D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER D 281 " --> pdb=" O THR D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 295 Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.522A pdb=" N THR D 318 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 360 through 365 Processing helix chain 'D' and resid 366 through 372 removed outlier: 4.074A pdb=" N VAL D 370 " --> pdb=" O GLY D 366 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS D 371 " --> pdb=" O PRO D 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 61 Processing helix chain 'E' and resid 82 through 91 removed outlier: 3.867A pdb=" N TRP E 86 " --> pdb=" O MET E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 127 removed outlier: 4.047A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 144 removed outlier: 4.065A pdb=" N SER E 141 " --> pdb=" O GLN E 137 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU E 142 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR E 143 " --> pdb=" O VAL E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 194 through 197 Processing helix chain 'E' and resid 202 through 210 Processing helix chain 'E' and resid 211 through 216 Processing helix chain 'E' and resid 223 through 233 removed outlier: 3.605A pdb=" N ALA E 228 " --> pdb=" O GLU E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 263 removed outlier: 3.967A pdb=" N ARG E 256 " --> pdb=" O ASN E 252 " (cutoff:3.500A) Proline residue: E 258 - end of helix removed outlier: 4.633A pdb=" N LEU E 261 " --> pdb=" O CYS E 257 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE E 262 " --> pdb=" O PRO E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 284 removed outlier: 3.811A pdb=" N TYR E 279 " --> pdb=" O HIS E 275 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER E 281 " --> pdb=" O THR E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 295 Processing helix chain 'E' and resid 308 through 321 removed outlier: 3.537A pdb=" N THR E 318 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU E 320 " --> pdb=" O GLU E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 360 through 365 Processing helix chain 'E' and resid 366 through 372 removed outlier: 4.078A pdb=" N VAL E 370 " --> pdb=" O GLY E 366 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS E 371 " --> pdb=" O PRO E 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 61 Processing helix chain 'F' and resid 82 through 91 removed outlier: 3.889A pdb=" N TRP F 86 " --> pdb=" O MET F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 126 removed outlier: 4.073A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 144 removed outlier: 4.079A pdb=" N SER F 141 " --> pdb=" O GLN F 137 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU F 142 " --> pdb=" O ALA F 138 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR F 143 " --> pdb=" O VAL F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 193 Processing helix chain 'F' and resid 194 through 196 No H-bonds generated for 'chain 'F' and resid 194 through 196' Processing helix chain 'F' and resid 202 through 210 Processing helix chain 'F' and resid 211 through 216 Processing helix chain 'F' and resid 223 through 233 removed outlier: 3.601A pdb=" N ALA F 228 " --> pdb=" O GLU F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 257 removed outlier: 3.949A pdb=" N ARG F 256 " --> pdb=" O ASN F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 263 removed outlier: 3.725A pdb=" N PHE F 262 " --> pdb=" O PRO F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 284 removed outlier: 3.851A pdb=" N TYR F 279 " --> pdb=" O HIS F 275 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER F 281 " --> pdb=" O THR F 277 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE F 282 " --> pdb=" O THR F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 296 Processing helix chain 'F' and resid 308 through 321 removed outlier: 3.609A pdb=" N THR F 318 " --> pdb=" O GLN F 314 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU F 320 " --> pdb=" O GLU F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 348 Processing helix chain 'F' and resid 360 through 365 Processing helix chain 'F' and resid 366 through 372 removed outlier: 4.068A pdb=" N VAL F 370 " --> pdb=" O GLY F 366 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS F 371 " --> pdb=" O PRO F 367 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 61 Processing helix chain 'G' and resid 82 through 91 removed outlier: 3.859A pdb=" N TRP G 86 " --> pdb=" O MET G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 126 removed outlier: 4.059A pdb=" N ARG G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 144 removed outlier: 4.050A pdb=" N SER G 141 " --> pdb=" O GLN G 137 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU G 142 " --> pdb=" O ALA G 138 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR G 143 " --> pdb=" O VAL G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 175 removed outlier: 4.289A pdb=" N ILE G 175 " --> pdb=" O PRO G 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 172 through 175' Processing helix chain 'G' and resid 181 through 193 Processing helix chain 'G' and resid 194 through 197 Processing helix chain 'G' and resid 202 through 210 Processing helix chain 'G' and resid 211 through 216 Processing helix chain 'G' and resid 223 through 233 removed outlier: 3.619A pdb=" N ALA G 228 " --> pdb=" O GLU G 224 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER G 232 " --> pdb=" O ALA G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 257 removed outlier: 3.972A pdb=" N ARG G 256 " --> pdb=" O ASN G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 263 removed outlier: 3.709A pdb=" N PHE G 262 " --> pdb=" O PRO G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 273 through 284 removed outlier: 3.767A pdb=" N TYR G 279 " --> pdb=" O HIS G 275 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER G 281 " --> pdb=" O THR G 277 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE G 282 " --> pdb=" O THR G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 290 through 296 Processing helix chain 'G' and resid 308 through 321 removed outlier: 3.570A pdb=" N THR G 318 " --> pdb=" O GLN G 314 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU G 320 " --> pdb=" O GLU G 316 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 348 Processing helix chain 'G' and resid 352 through 356 removed outlier: 3.647A pdb=" N MET G 355 " --> pdb=" O PHE G 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 360 through 365 Processing helix chain 'G' and resid 366 through 372 removed outlier: 4.086A pdb=" N VAL G 370 " --> pdb=" O GLY G 366 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS G 371 " --> pdb=" O PRO G 367 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 61 Processing helix chain 'H' and resid 82 through 91 removed outlier: 3.868A pdb=" N TRP H 86 " --> pdb=" O MET H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 127 removed outlier: 4.059A pdb=" N ARG H 116 " --> pdb=" O PRO H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 144 removed outlier: 4.079A pdb=" N SER H 141 " --> pdb=" O GLN H 137 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU H 142 " --> pdb=" O ALA H 138 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR H 143 " --> pdb=" O VAL H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 193 Processing helix chain 'H' and resid 194 through 197 Processing helix chain 'H' and resid 202 through 210 Processing helix chain 'H' and resid 211 through 216 Processing helix chain 'H' and resid 223 through 233 removed outlier: 3.605A pdb=" N ALA H 228 " --> pdb=" O GLU H 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 263 removed outlier: 3.997A pdb=" N ARG H 256 " --> pdb=" O ASN H 252 " (cutoff:3.500A) Proline residue: H 258 - end of helix removed outlier: 4.594A pdb=" N LEU H 261 " --> pdb=" O CYS H 257 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE H 262 " --> pdb=" O PRO H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 273 through 284 removed outlier: 3.871A pdb=" N TYR H 279 " --> pdb=" O HIS H 275 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER H 281 " --> pdb=" O THR H 277 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE H 282 " --> pdb=" O THR H 278 " (cutoff:3.500A) Processing helix chain 'H' and resid 290 through 295 Processing helix chain 'H' and resid 308 through 321 removed outlier: 3.560A pdb=" N THR H 318 " --> pdb=" O GLN H 314 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU H 320 " --> pdb=" O GLU H 316 " (cutoff:3.500A) Processing helix chain 'H' and resid 337 through 348 Processing helix chain 'H' and resid 360 through 365 Processing helix chain 'H' and resid 366 through 372 removed outlier: 4.036A pdb=" N VAL H 370 " --> pdb=" O GLY H 366 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS H 371 " --> pdb=" O PRO H 367 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain 'D' and resid 29 through 32 removed outlier: 3.572A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=C, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.631A pdb=" N VAL D 163 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL D 152 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'E' and resid 29 through 32 removed outlier: 3.596A pdb=" N THR E 106 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=F, first strand: chain 'E' and resid 169 through 170 removed outlier: 3.629A pdb=" N VAL E 163 " --> pdb=" O VAL E 152 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL E 152 " --> pdb=" O VAL E 163 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) Processing sheet with id=G, first strand: chain 'F' and resid 29 through 32 removed outlier: 3.614A pdb=" N THR F 106 " --> pdb=" O CYS F 10 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N THR F 103 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ALA F 135 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU F 105 " --> pdb=" O ALA F 135 " (cutoff:3.500A) Processing sheet with id=H, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=I, first strand: chain 'F' and resid 169 through 170 removed outlier: 3.608A pdb=" N VAL F 163 " --> pdb=" O VAL F 152 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL F 152 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) Processing sheet with id=J, first strand: chain 'G' and resid 29 through 32 removed outlier: 3.589A pdb=" N THR G 106 " --> pdb=" O CYS G 10 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N THR G 103 " --> pdb=" O TYR G 133 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ALA G 135 " --> pdb=" O THR G 103 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU G 105 " --> pdb=" O ALA G 135 " (cutoff:3.500A) Processing sheet with id=K, first strand: chain 'G' and resid 71 through 72 Processing sheet with id=L, first strand: chain 'G' and resid 169 through 170 removed outlier: 3.649A pdb=" N VAL G 163 " --> pdb=" O VAL G 152 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL G 152 " --> pdb=" O VAL G 163 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE G 151 " --> pdb=" O VAL G 298 " (cutoff:3.500A) Processing sheet with id=M, first strand: chain 'H' and resid 29 through 32 removed outlier: 3.609A pdb=" N THR H 106 " --> pdb=" O CYS H 10 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N THR H 103 " --> pdb=" O TYR H 133 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ALA H 135 " --> pdb=" O THR H 103 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU H 105 " --> pdb=" O ALA H 135 " (cutoff:3.500A) Processing sheet with id=N, first strand: chain 'H' and resid 71 through 72 Processing sheet with id=O, first strand: chain 'H' and resid 169 through 170 removed outlier: 3.643A pdb=" N VAL H 163 " --> pdb=" O VAL H 152 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL H 152 " --> pdb=" O VAL H 163 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE H 151 " --> pdb=" O VAL H 298 " (cutoff:3.500A) 419 hydrogen bonds defined for protein. 1185 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: 4.38 Time building geometry restraints manager: 6.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 4526 1.34 - 1.48: 4024 1.48 - 1.63: 6385 1.63 - 1.77: 21 1.77 - 1.91: 164 Bond restraints: 15120 Sorted by residual: bond pdb=" C LEU D 171 " pdb=" N PRO D 172 " ideal model delta sigma weight residual 1.331 1.383 -0.052 7.90e-03 1.60e+04 4.29e+01 bond pdb=" C LEU H 171 " pdb=" N PRO H 172 " ideal model delta sigma weight residual 1.331 1.382 -0.050 7.90e-03 1.60e+04 4.05e+01 bond pdb=" C LEU F 171 " pdb=" N PRO F 172 " ideal model delta sigma weight residual 1.331 1.379 -0.047 7.90e-03 1.60e+04 3.55e+01 bond pdb=" CA ILE E 250 " pdb=" C ILE E 250 " ideal model delta sigma weight residual 1.526 1.474 0.052 9.00e-03 1.23e+04 3.32e+01 bond pdb=" C LEU E 171 " pdb=" N PRO E 172 " ideal model delta sigma weight residual 1.331 1.376 -0.045 7.90e-03 1.60e+04 3.24e+01 ... (remaining 15115 not shown) Histogram of bond angle deviations from ideal: 98.44 - 105.87: 547 105.87 - 113.29: 7617 113.29 - 120.72: 6773 120.72 - 128.15: 5453 128.15 - 135.58: 125 Bond angle restraints: 20515 Sorted by residual: angle pdb=" C VAL F 129 " pdb=" N PRO F 130 " pdb=" CA PRO F 130 " ideal model delta sigma weight residual 119.19 126.79 -7.60 1.06e+00 8.90e-01 5.13e+01 angle pdb=" C ALA D 108 " pdb=" N PRO D 109 " pdb=" CA PRO D 109 " ideal model delta sigma weight residual 119.78 127.02 -7.24 1.03e+00 9.43e-01 4.94e+01 angle pdb=" N ALA G 138 " pdb=" CA ALA G 138 " pdb=" C ALA G 138 " ideal model delta sigma weight residual 111.28 118.53 -7.25 1.09e+00 8.42e-01 4.42e+01 angle pdb=" C ALA G 108 " pdb=" N PRO G 109 " pdb=" CA PRO G 109 " ideal model delta sigma weight residual 119.78 126.55 -6.77 1.03e+00 9.43e-01 4.32e+01 angle pdb=" N ALA D 138 " pdb=" CA ALA D 138 " pdb=" C ALA D 138 " ideal model delta sigma weight residual 111.36 118.09 -6.73 1.09e+00 8.42e-01 3.81e+01 ... (remaining 20510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.49: 8650 35.49 - 70.97: 411 70.97 - 106.46: 34 106.46 - 141.94: 5 141.94 - 177.43: 5 Dihedral angle restraints: 9105 sinusoidal: 3685 harmonic: 5420 Sorted by residual: dihedral pdb=" C5' ADP G 401 " pdb=" O5' ADP G 401 " pdb=" PA ADP G 401 " pdb=" O2A ADP G 401 " ideal model delta sinusoidal sigma weight residual -60.00 117.43 -177.43 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP D 401 " pdb=" O5' ADP D 401 " pdb=" PA ADP D 401 " pdb=" O2A ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 117.43 -177.43 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP F 401 " pdb=" O5' ADP F 401 " pdb=" PA ADP F 401 " pdb=" O2A ADP F 401 " ideal model delta sinusoidal sigma weight residual -60.00 117.33 -177.32 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 9102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1407 0.093 - 0.185: 657 0.185 - 0.278: 181 0.278 - 0.370: 24 0.370 - 0.463: 6 Chirality restraints: 2275 Sorted by residual: chirality pdb=" CA PRO E 243 " pdb=" N PRO E 243 " pdb=" C PRO E 243 " pdb=" CB PRO E 243 " both_signs ideal model delta sigma weight residual False 2.72 2.26 0.46 2.00e-01 2.50e+01 5.36e+00 chirality pdb=" CA PRO F 243 " pdb=" N PRO F 243 " pdb=" C PRO F 243 " pdb=" CB PRO F 243 " both_signs ideal model delta sigma weight residual False 2.72 2.27 0.45 2.00e-01 2.50e+01 5.03e+00 chirality pdb=" CA PRO H 243 " pdb=" N PRO H 243 " pdb=" C PRO H 243 " pdb=" CB PRO H 243 " both_signs ideal model delta sigma weight residual False 2.72 2.29 0.43 2.00e-01 2.50e+01 4.54e+00 ... (remaining 2272 not shown) Planarity restraints: 2630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 166 " -0.071 2.00e-02 2.50e+03 3.56e-02 2.53e+01 pdb=" CG TYR D 166 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR D 166 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR D 166 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR D 166 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR D 166 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR D 166 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR D 166 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 166 " 0.061 2.00e-02 2.50e+03 3.07e-02 1.88e+01 pdb=" CG TYR E 166 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR E 166 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR E 166 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR E 166 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR E 166 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR E 166 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR E 166 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 166 " -0.060 2.00e-02 2.50e+03 3.03e-02 1.83e+01 pdb=" CG TYR H 166 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR H 166 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR H 166 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR H 166 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR H 166 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR H 166 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR H 166 " -0.027 2.00e-02 2.50e+03 ... (remaining 2627 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 784 2.68 - 3.24: 16908 3.24 - 3.79: 24664 3.79 - 4.35: 32343 4.35 - 4.90: 50125 Nonbonded interactions: 124824 Sorted by model distance: nonbonded pdb=" O SER F 350 " pdb=" N PHE F 352 " model vdw 2.125 2.520 nonbonded pdb=" O TYR H 362 " pdb=" O ALA H 365 " model vdw 2.131 3.040 nonbonded pdb=" O TYR F 362 " pdb=" O ALA F 365 " model vdw 2.140 3.040 nonbonded pdb=" O TYR G 362 " pdb=" O ALA G 365 " model vdw 2.154 3.040 nonbonded pdb=" O SER D 350 " pdb=" N PHE D 352 " model vdw 2.160 2.520 ... (remaining 124819 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 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set refine NCS operators NCS operators will be refined. 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: 0.340 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: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 41.660 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 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 : 0.018 0.120 15120 Z= 1.171 Angle : 1.668 11.796 20515 Z= 1.105 Chirality : 0.109 0.463 2275 Planarity : 0.007 0.098 2630 Dihedral : 19.470 177.430 5635 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 76.17 Ramachandran Plot: Outliers : 6.06 % Allowed : 6.43 % Favored : 87.51 % Rotamer: Outliers : 14.53 % Allowed : 14.65 % Favored : 70.82 % 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: -1.59 (0.17), residues: 1865 helix: -0.26 (0.22), residues: 500 sheet: 0.08 (0.37), residues: 205 loop : -1.71 (0.16), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.009 TRP G 356 HIS 0.004 0.001 HIS E 101 PHE 0.030 0.005 PHE G 375 TYR 0.071 0.009 TYR D 166 ARG 0.012 0.002 ARG E 290 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 60 time to evaluate : 0.299 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: D 76 ILE cc_start: 0.8806 (mt) cc_final: 0.8105 (mt) REVERT: D 82 MET cc_start: 0.8828 (ttt) cc_final: 0.8509 (ttm) REVERT: D 116 ARG cc_start: 0.6769 (mtp180) cc_final: 0.6181 (mtp-110) REVERT: D 147 ARG cc_start: 0.7676 (mpp-170) cc_final: 0.7265 (mpp-170) REVERT: D 371 HIS cc_start: 0.7631 (OUTLIER) cc_final: 0.7148 (t-90) REVERT: D 373 LYS cc_start: 0.6486 (OUTLIER) cc_final: 0.6278 (tmmt) outliers start: 46 outliers final: 19 residues processed: 96 average time/residue: 0.1666 time to fit residues: 18.9416 Evaluate side-chains 60 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 39 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 20.0000 chunk 140 optimal weight: 20.0000 chunk 77 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 94 optimal weight: 20.0000 chunk 74 optimal weight: 40.0000 chunk 145 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 88 optimal weight: 0.0980 chunk 107 optimal weight: 9.9990 chunk 168 optimal weight: 20.0000 overall best weight: 6.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 59 GLN F 87 HIS ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN F 296 ASN ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 353 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15120 Z= 0.272 Angle : 0.917 9.432 20515 Z= 0.460 Chirality : 0.047 0.173 2275 Planarity : 0.006 0.039 2630 Dihedral : 8.553 112.954 2095 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 28.67 Ramachandran Plot: Outliers : 1.88 % Allowed : 10.99 % Favored : 87.13 % Rotamer: Outliers : 0.63 % Allowed : 8.49 % Favored : 90.88 % 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: -1.64 (0.19), residues: 1865 helix: 0.06 (0.20), residues: 645 sheet: -0.11 (0.36), residues: 230 loop : -2.21 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 340 HIS 0.013 0.002 HIS F 40 PHE 0.012 0.002 PHE G 255 TYR 0.035 0.002 TYR H 169 ARG 0.004 0.001 ARG G 254 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 64 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 25 ASP cc_start: 0.8560 (m-30) cc_final: 0.8051 (p0) REVERT: F 116 ARG cc_start: 0.7268 (mtp180) cc_final: 0.6886 (mtp-110) REVERT: F 134 VAL cc_start: 0.9201 (t) cc_final: 0.8894 (t) REVERT: F 147 ARG cc_start: 0.8010 (mpp-170) cc_final: 0.7306 (mpp-170) REVERT: F 211 ASP cc_start: 0.8334 (p0) cc_final: 0.7544 (p0) REVERT: F 305 MET cc_start: 0.8793 (tpp) cc_final: 0.8544 (tpp) outliers start: 2 outliers final: 0 residues processed: 66 average time/residue: 0.1657 time to fit residues: 13.0648 Evaluate side-chains 41 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 7.9990 chunk 52 optimal weight: 8.9990 chunk 139 optimal weight: 20.0000 chunk 114 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 168 optimal weight: 20.0000 chunk 181 optimal weight: 9.9990 chunk 149 optimal weight: 0.7980 chunk 166 optimal weight: 7.9990 chunk 57 optimal weight: 20.0000 chunk 135 optimal weight: 30.0000 overall best weight: 7.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 12 ASN ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 GLN F 314 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.5351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15120 Z= 0.240 Angle : 0.810 8.176 20515 Z= 0.408 Chirality : 0.045 0.159 2275 Planarity : 0.005 0.047 2630 Dihedral : 7.326 87.559 2095 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 26.97 Ramachandran Plot: Outliers : 1.34 % Allowed : 10.99 % Favored : 87.67 % Rotamer: Outliers : 0.31 % Allowed : 5.97 % Favored : 93.71 % 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: -1.86 (0.18), residues: 1865 helix: -0.73 (0.18), residues: 685 sheet: 0.63 (0.43), residues: 180 loop : -2.01 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 340 HIS 0.004 0.002 HIS G 275 PHE 0.013 0.002 PHE D 375 TYR 0.012 0.001 TYR D 294 ARG 0.003 0.001 ARG H 147 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 25 ASP cc_start: 0.8528 (m-30) cc_final: 0.8057 (p0) REVERT: F 184 ASP cc_start: 0.9158 (p0) cc_final: 0.8448 (t70) REVERT: F 211 ASP cc_start: 0.8320 (p0) cc_final: 0.7144 (t0) REVERT: F 269 MET cc_start: 0.7554 (mpp) cc_final: 0.7059 (mmp) outliers start: 1 outliers final: 0 residues processed: 58 average time/residue: 0.1874 time to fit residues: 12.8379 Evaluate side-chains 43 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 10.0000 chunk 126 optimal weight: 0.2980 chunk 87 optimal weight: 0.0270 chunk 18 optimal weight: 2.9990 chunk 80 optimal weight: 20.0000 chunk 113 optimal weight: 3.9990 chunk 168 optimal weight: 20.0000 chunk 178 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 160 optimal weight: 0.9990 chunk 48 optimal weight: 20.0000 overall best weight: 1.2644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 ASN ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.6123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15120 Z= 0.179 Angle : 0.801 10.162 20515 Z= 0.401 Chirality : 0.045 0.157 2275 Planarity : 0.007 0.087 2630 Dihedral : 6.841 74.189 2095 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 19.81 Ramachandran Plot: Outliers : 1.07 % Allowed : 10.99 % Favored : 87.94 % Rotamer: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % 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: -2.02 (0.18), residues: 1865 helix: -0.74 (0.19), residues: 620 sheet: -0.52 (0.33), residues: 260 loop : -2.00 (0.18), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 340 HIS 0.004 0.001 HIS F 161 PHE 0.006 0.001 PHE H 127 TYR 0.010 0.001 TYR F 198 ARG 0.013 0.001 ARG H 147 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 9 VAL cc_start: 0.7530 (t) cc_final: 0.6920 (t) REVERT: F 44 MET cc_start: 0.6434 (mmm) cc_final: 0.4555 (mtm) REVERT: F 67 LEU cc_start: 0.9338 (mp) cc_final: 0.9129 (tp) REVERT: F 104 LEU cc_start: 0.9030 (tp) cc_final: 0.8255 (pp) REVERT: F 132 MET cc_start: 0.6149 (ppp) cc_final: 0.5809 (tmm) REVERT: F 184 ASP cc_start: 0.9093 (p0) cc_final: 0.8438 (t70) REVERT: F 211 ASP cc_start: 0.8233 (p0) cc_final: 0.7124 (t0) REVERT: F 217 CYS cc_start: 0.7023 (p) cc_final: 0.6054 (p) REVERT: F 269 MET cc_start: 0.8190 (mpp) cc_final: 0.7893 (mmm) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1423 time to fit residues: 10.2164 Evaluate side-chains 46 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 30.0000 chunk 101 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 chunk 73 optimal weight: 0.0040 chunk 152 optimal weight: 40.0000 chunk 123 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 91 optimal weight: 0.0060 chunk 160 optimal weight: 3.9990 chunk 45 optimal weight: 20.0000 overall best weight: 0.5408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 173 HIS ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.6599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15120 Z= 0.170 Angle : 0.760 7.670 20515 Z= 0.378 Chirality : 0.044 0.158 2275 Planarity : 0.006 0.051 2630 Dihedral : 6.187 56.464 2095 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 1.07 % Allowed : 10.46 % Favored : 88.47 % Rotamer: Outliers : 0.31 % Allowed : 2.83 % Favored : 96.86 % 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: -2.10 (0.18), residues: 1865 helix: -0.67 (0.18), residues: 630 sheet: -0.57 (0.33), residues: 260 loop : -2.17 (0.18), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP H 86 HIS 0.002 0.001 HIS H 88 PHE 0.011 0.002 PHE D 200 TYR 0.010 0.001 TYR D 306 ARG 0.004 0.001 ARG H 256 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 67 LEU cc_start: 0.9392 (mp) cc_final: 0.9186 (tp) REVERT: F 105 LEU cc_start: 0.8294 (tp) cc_final: 0.7946 (mp) REVERT: F 132 MET cc_start: 0.6540 (ppp) cc_final: 0.6292 (ppp) REVERT: F 184 ASP cc_start: 0.9018 (p0) cc_final: 0.8446 (t70) REVERT: F 211 ASP cc_start: 0.8340 (p0) cc_final: 0.7170 (t0) REVERT: F 269 MET cc_start: 0.7765 (mpp) cc_final: 0.7300 (mmp) REVERT: F 316 GLU cc_start: 0.8903 (mm-30) cc_final: 0.7987 (tp30) outliers start: 1 outliers final: 1 residues processed: 57 average time/residue: 0.1217 time to fit residues: 8.8096 Evaluate side-chains 48 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 7.9990 chunk 161 optimal weight: 0.0770 chunk 35 optimal weight: 0.0070 chunk 104 optimal weight: 7.9990 chunk 44 optimal weight: 0.6980 chunk 178 optimal weight: 2.9990 chunk 148 optimal weight: 20.0000 chunk 82 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 59 optimal weight: 20.0000 chunk 93 optimal weight: 0.0040 overall best weight: 0.7570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.6975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15120 Z= 0.167 Angle : 0.769 11.366 20515 Z= 0.386 Chirality : 0.043 0.154 2275 Planarity : 0.005 0.047 2630 Dihedral : 5.921 44.302 2095 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 1.07 % Allowed : 10.72 % Favored : 88.20 % Rotamer: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % 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: -1.97 (0.18), residues: 1865 helix: -0.59 (0.19), residues: 615 sheet: -0.22 (0.33), residues: 250 loop : -2.13 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 86 HIS 0.007 0.001 HIS E 161 PHE 0.013 0.001 PHE D 200 TYR 0.008 0.001 TYR H 166 ARG 0.002 0.000 ARG F 177 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 67 LEU cc_start: 0.9400 (mp) cc_final: 0.9181 (tp) REVERT: F 184 ASP cc_start: 0.9046 (p0) cc_final: 0.8455 (t70) REVERT: F 211 ASP cc_start: 0.8348 (p0) cc_final: 0.7259 (t0) REVERT: F 269 MET cc_start: 0.8218 (mpp) cc_final: 0.7919 (mmm) REVERT: F 316 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8121 (tp30) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1256 time to fit residues: 8.5873 Evaluate side-chains 44 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 101 optimal weight: 0.8980 chunk 130 optimal weight: 0.1980 chunk 150 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 178 optimal weight: 0.0770 chunk 111 optimal weight: 30.0000 chunk 108 optimal weight: 20.0000 chunk 82 optimal weight: 0.5980 chunk 110 optimal weight: 5.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 HIS ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.7296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15120 Z= 0.162 Angle : 0.759 9.184 20515 Z= 0.379 Chirality : 0.045 0.157 2275 Planarity : 0.005 0.048 2630 Dihedral : 5.646 38.916 2095 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.80 % Allowed : 9.92 % Favored : 89.28 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % 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: -2.17 (0.17), residues: 1865 helix: -0.87 (0.18), residues: 625 sheet: 0.04 (0.32), residues: 280 loop : -2.35 (0.17), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 86 HIS 0.004 0.001 HIS H 161 PHE 0.008 0.001 PHE F 31 TYR 0.009 0.001 TYR E 166 ARG 0.003 0.000 ARG D 177 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 132 MET cc_start: 0.6386 (ppp) cc_final: 0.5889 (tmm) REVERT: F 184 ASP cc_start: 0.9044 (p0) cc_final: 0.8464 (t70) REVERT: F 211 ASP cc_start: 0.8369 (p0) cc_final: 0.7234 (t0) REVERT: F 269 MET cc_start: 0.8208 (mpp) cc_final: 0.7680 (mmp) REVERT: F 316 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8135 (tp30) REVERT: F 325 MET cc_start: 0.8182 (mmp) cc_final: 0.7782 (mmm) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1292 time to fit residues: 8.8465 Evaluate side-chains 45 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 30.0000 chunk 106 optimal weight: 0.0060 chunk 53 optimal weight: 0.0040 chunk 35 optimal weight: 20.0000 chunk 34 optimal weight: 20.0000 chunk 113 optimal weight: 0.0370 chunk 121 optimal weight: 0.0970 chunk 88 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 140 optimal weight: 20.0000 chunk 162 optimal weight: 0.9980 overall best weight: 0.2284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.7720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15120 Z= 0.167 Angle : 0.752 7.864 20515 Z= 0.370 Chirality : 0.045 0.182 2275 Planarity : 0.005 0.048 2630 Dihedral : 5.672 35.561 2095 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.80 % Allowed : 10.19 % Favored : 89.01 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % 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: -2.07 (0.17), residues: 1865 helix: -0.72 (0.19), residues: 630 sheet: 0.42 (0.38), residues: 200 loop : -2.25 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 86 HIS 0.003 0.001 HIS H 161 PHE 0.008 0.001 PHE D 31 TYR 0.008 0.001 TYR G 69 ARG 0.005 0.001 ARG D 335 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 184 ASP cc_start: 0.9057 (p0) cc_final: 0.8495 (t0) REVERT: F 211 ASP cc_start: 0.8275 (p0) cc_final: 0.6938 (t70) REVERT: F 269 MET cc_start: 0.8189 (mpp) cc_final: 0.7887 (mmm) REVERT: F 316 GLU cc_start: 0.8949 (mm-30) cc_final: 0.8224 (tp30) REVERT: F 325 MET cc_start: 0.8282 (mmp) cc_final: 0.7894 (mmm) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1283 time to fit residues: 9.1288 Evaluate side-chains 47 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 20.0000 chunk 155 optimal weight: 0.0070 chunk 166 optimal weight: 9.9990 chunk 100 optimal weight: 0.5980 chunk 72 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 50 optimal weight: 0.0870 chunk 150 optimal weight: 10.0000 chunk 157 optimal weight: 7.9990 chunk 165 optimal weight: 0.0770 chunk 109 optimal weight: 6.9990 overall best weight: 1.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 ASN ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.7902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15120 Z= 0.165 Angle : 0.783 7.933 20515 Z= 0.385 Chirality : 0.045 0.198 2275 Planarity : 0.005 0.047 2630 Dihedral : 5.589 31.565 2095 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 1.07 % Allowed : 9.65 % Favored : 89.28 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % 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: -2.15 (0.18), residues: 1865 helix: -1.03 (0.18), residues: 660 sheet: 1.11 (0.44), residues: 160 loop : -2.20 (0.17), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP H 86 HIS 0.003 0.001 HIS F 161 PHE 0.008 0.001 PHE D 31 TYR 0.009 0.001 TYR G 166 ARG 0.003 0.000 ARG D 335 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 MET cc_start: 0.5827 (mmm) cc_final: 0.3040 (mtm) REVERT: F 132 MET cc_start: 0.6259 (ppp) cc_final: 0.5906 (tmm) REVERT: F 184 ASP cc_start: 0.9083 (p0) cc_final: 0.8501 (t70) REVERT: F 225 ASN cc_start: 0.8111 (t0) cc_final: 0.7817 (t0) REVERT: F 269 MET cc_start: 0.8240 (mpp) cc_final: 0.7885 (mmm) REVERT: F 325 MET cc_start: 0.8353 (mmp) cc_final: 0.7976 (mmm) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1066 time to fit residues: 7.5795 Evaluate side-chains 41 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 184 optimal weight: 7.9990 chunk 169 optimal weight: 20.0000 chunk 146 optimal weight: 0.0980 chunk 15 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 173 HIS ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.8203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15120 Z= 0.162 Angle : 0.824 13.106 20515 Z= 0.400 Chirality : 0.046 0.183 2275 Planarity : 0.005 0.047 2630 Dihedral : 5.490 31.053 2095 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 1.07 % Allowed : 10.72 % Favored : 88.20 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: -2.14 (0.18), residues: 1865 helix: -0.88 (0.19), residues: 670 sheet: 0.51 (0.38), residues: 195 loop : -2.28 (0.17), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP H 86 HIS 0.003 0.001 HIS H 88 PHE 0.008 0.001 PHE H 262 TYR 0.012 0.001 TYR D 306 ARG 0.003 0.001 ARG D 210 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 MET cc_start: 0.5871 (mmm) cc_final: 0.5546 (mmp) REVERT: F 132 MET cc_start: 0.6451 (ppp) cc_final: 0.6032 (tmm) REVERT: F 184 ASP cc_start: 0.9059 (p0) cc_final: 0.8468 (t70) REVERT: F 225 ASN cc_start: 0.7966 (t0) cc_final: 0.7647 (t0) REVERT: F 269 MET cc_start: 0.8119 (mpp) cc_final: 0.7545 (mmp) REVERT: F 316 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8141 (tp30) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1083 time to fit residues: 7.4519 Evaluate side-chains 40 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 21 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 chunk 146 optimal weight: 8.9990 chunk 61 optimal weight: 0.0020 chunk 150 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 129 optimal weight: 10.0000 overall best weight: 4.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.071890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.065237 restraints weight = 15146.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.066567 restraints weight = 9698.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.067607 restraints weight = 6727.880| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.8190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15120 Z= 0.184 Angle : 0.785 10.303 20515 Z= 0.386 Chirality : 0.045 0.175 2275 Planarity : 0.005 0.047 2630 Dihedral : 5.531 35.035 2095 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 1.07 % Allowed : 10.46 % Favored : 88.47 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: -2.04 (0.18), residues: 1865 helix: -0.92 (0.19), residues: 660 sheet: 0.41 (0.37), residues: 200 loop : -2.08 (0.18), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP G 86 HIS 0.003 0.001 HIS E 173 PHE 0.010 0.001 PHE H 262 TYR 0.006 0.001 TYR F 166 ARG 0.003 0.001 ARG H 177 =============================================================================== Job complete usr+sys time: 1940.81 seconds wall clock time: 36 minutes 13.94 seconds (2173.94 seconds total)