Starting phenix.real_space_refine on Thu Nov 16 02:27:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oze_17306/11_2023/8oze_17306.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oze_17306/11_2023/8oze_17306.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oze_17306/11_2023/8oze_17306.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oze_17306/11_2023/8oze_17306.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oze_17306/11_2023/8oze_17306.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oze_17306/11_2023/8oze_17306.pdb" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 502 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 74 5.49 5 S 40 5.16 5 C 8420 2.51 5 N 2244 2.21 5 O 2656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 474": "OD1" <-> "OD2" Residue "F TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 474": "OD1" <-> "OD2" Residue "H TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 13434 Number of models: 1 Model: "" Number of chains: 8 Chain: "N" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 435 Classifications: {'RNA': 20} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 12, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 18} Chain: "P" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 339 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "E" Number of atoms: 2122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2122 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 8, 'TRANS': 242} Chain: "F" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Chain: "G" Number of atoms: 2122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2122 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 8, 'TRANS': 242} Chain: "H" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Chain: "A" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 435 Classifications: {'RNA': 20} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 12, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 18} Chain: "B" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 339 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Time building chain proxies: 7.18, per 1000 atoms: 0.53 Number of scatterers: 13434 At special positions: 0 Unit cell: (153.67, 129.47, 84.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 74 15.00 O 2656 8.00 N 2244 7.00 C 8420 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: 5.58 Conformation dependent library (CDL) restraints added in 2.4 seconds 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2748 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 14 sheets defined 35.9% alpha, 16.9% beta 21 base pairs and 58 stacking pairs defined. Time for finding SS restraints: 4.95 Creating SS restraints... Processing helix chain 'E' and resid 190 through 194 Processing helix chain 'E' and resid 199 through 203 removed outlier: 3.556A pdb=" N GLU E 202 " --> pdb=" O ASP E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 233 removed outlier: 3.590A pdb=" N GLU E 231 " --> pdb=" O PRO E 228 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N THR E 232 " --> pdb=" O LYS E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 238 Processing helix chain 'E' and resid 243 through 249 Processing helix chain 'E' and resid 257 through 280 removed outlier: 3.504A pdb=" N ARG E 263 " --> pdb=" O ALA E 259 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU E 264 " --> pdb=" O GLU E 260 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE E 265 " --> pdb=" O CYS E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 366 Processing helix chain 'E' and resid 369 through 385 removed outlier: 3.834A pdb=" N LYS E 376 " --> pdb=" O THR E 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 17 No H-bonds generated for 'chain 'F' and resid 15 through 17' Processing helix chain 'F' and resid 22 through 30 Processing helix chain 'F' and resid 46 through 62 removed outlier: 3.643A pdb=" N ILE F 52 " --> pdb=" O GLN F 48 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS F 62 " --> pdb=" O ASP F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 83 Processing helix chain 'F' and resid 97 through 104 removed outlier: 3.717A pdb=" N PHE F 104 " --> pdb=" O ASP F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 131 removed outlier: 4.123A pdb=" N LYS F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 150 removed outlier: 3.568A pdb=" N TYR F 148 " --> pdb=" O PRO F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 162 Processing helix chain 'F' and resid 205 through 214 removed outlier: 3.574A pdb=" N LEU F 214 " --> pdb=" O PHE F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 264 Processing helix chain 'F' and resid 331 through 351 removed outlier: 3.586A pdb=" N GLN F 349 " --> pdb=" O SER F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 377 removed outlier: 3.564A pdb=" N VAL F 376 " --> pdb=" O ALA F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 430 Processing helix chain 'F' and resid 451 through 463 Processing helix chain 'F' and resid 477 through 491 Processing helix chain 'F' and resid 502 through 506 removed outlier: 3.592A pdb=" N TYR F 505 " --> pdb=" O ALA F 502 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 194 Processing helix chain 'G' and resid 199 through 203 removed outlier: 3.556A pdb=" N GLU G 202 " --> pdb=" O ASP G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 233 removed outlier: 3.590A pdb=" N GLU G 231 " --> pdb=" O PRO G 228 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR G 232 " --> pdb=" O LYS G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 238 Processing helix chain 'G' and resid 243 through 249 Processing helix chain 'G' and resid 257 through 280 removed outlier: 3.504A pdb=" N ARG G 263 " --> pdb=" O ALA G 259 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU G 264 " --> pdb=" O GLU G 260 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE G 265 " --> pdb=" O CYS G 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 353 through 366 Processing helix chain 'G' and resid 369 through 385 removed outlier: 3.834A pdb=" N LYS G 376 " --> pdb=" O THR G 372 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 17 No H-bonds generated for 'chain 'H' and resid 15 through 17' Processing helix chain 'H' and resid 22 through 30 Processing helix chain 'H' and resid 46 through 62 removed outlier: 3.642A pdb=" N ILE H 52 " --> pdb=" O GLN H 48 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS H 62 " --> pdb=" O ASP H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 83 Processing helix chain 'H' and resid 97 through 104 removed outlier: 3.718A pdb=" N PHE H 104 " --> pdb=" O ASP H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 131 removed outlier: 4.123A pdb=" N LYS H 124 " --> pdb=" O LEU H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 150 removed outlier: 3.567A pdb=" N TYR H 148 " --> pdb=" O PRO H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 158 through 162 Processing helix chain 'H' and resid 205 through 214 removed outlier: 3.575A pdb=" N LEU H 214 " --> pdb=" O PHE H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 248 through 264 Processing helix chain 'H' and resid 331 through 351 removed outlier: 3.586A pdb=" N GLN H 349 " --> pdb=" O SER H 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 366 through 377 removed outlier: 3.564A pdb=" N VAL H 376 " --> pdb=" O ALA H 372 " (cutoff:3.500A) Processing helix chain 'H' and resid 427 through 430 Processing helix chain 'H' and resid 451 through 463 Processing helix chain 'H' and resid 477 through 491 Processing helix chain 'H' and resid 502 through 506 removed outlier: 3.592A pdb=" N TYR H 505 " --> pdb=" O ALA H 502 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 169 through 180 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 169 through 180 current: chain 'E' and resid 317 through 328 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 334 through 344 current: chain 'E' and resid 400 through 412 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 2 through 6 current: chain 'F' and resid 297 through 305 removed outlier: 7.400A pdb=" N CYS F 298 " --> pdb=" O GLY F 318 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N GLY F 318 " --> pdb=" O CYS F 298 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA F 300 " --> pdb=" O GLU F 316 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 311 through 321 current: chain 'F' and resid 382 through 389 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 382 through 389 current: chain 'F' and resid 417 through 420 Processing sheet with id=AA2, first strand: chain 'E' and resid 208 through 210 Processing sheet with id=AA3, first strand: chain 'E' and resid 283 through 286 Processing sheet with id=AA4, first strand: chain 'E' and resid 304 through 305 removed outlier: 3.639A pdb=" N PHE E 305 " --> pdb=" O THR E 308 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 19 through 20 Processing sheet with id=AA6, first strand: chain 'F' and resid 92 through 95 removed outlier: 6.346A pdb=" N GLY F 42 " --> pdb=" O PHE F 140 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ILE F 142 " --> pdb=" O GLY F 42 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE F 44 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TRP F 139 " --> pdb=" O GLN F 222 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N PHE F 224 " --> pdb=" O TRP F 139 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL F 141 " --> pdb=" O PHE F 224 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 425 through 426 removed outlier: 4.035A pdb=" N THR F 431 " --> pdb=" O VAL F 426 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 169 through 180 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 169 through 180 current: chain 'G' and resid 317 through 328 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 334 through 344 current: chain 'G' and resid 400 through 412 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 2 through 6 current: chain 'H' and resid 297 through 305 removed outlier: 7.400A pdb=" N CYS H 298 " --> pdb=" O GLY H 318 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N GLY H 318 " --> pdb=" O CYS H 298 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA H 300 " --> pdb=" O GLU H 316 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 311 through 321 current: chain 'H' and resid 382 through 389 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 382 through 389 current: chain 'H' and resid 417 through 420 Processing sheet with id=AA9, first strand: chain 'G' and resid 208 through 210 Processing sheet with id=AB1, first strand: chain 'G' and resid 283 through 286 Processing sheet with id=AB2, first strand: chain 'G' and resid 304 through 305 removed outlier: 3.639A pdb=" N PHE G 305 " --> pdb=" O THR G 308 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 18 through 20 removed outlier: 3.557A pdb=" N GLN H 18 " --> pdb=" O PHE H 14 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 92 through 95 removed outlier: 6.346A pdb=" N GLY H 42 " --> pdb=" O PHE H 140 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ILE H 142 " --> pdb=" O GLY H 42 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE H 44 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TRP H 139 " --> pdb=" O GLN H 222 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N PHE H 224 " --> pdb=" O TRP H 139 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL H 141 " --> pdb=" O PHE H 224 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 425 through 426 removed outlier: 4.034A pdb=" N THR H 431 " --> pdb=" O VAL H 426 " (cutoff:3.500A) 409 hydrogen bonds defined for protein. 1095 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 58 stacking parallelities Total time for adding SS restraints: 3.70 Time building geometry restraints manager: 6.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2871 1.33 - 1.45: 3531 1.45 - 1.57: 7324 1.57 - 1.69: 144 1.69 - 1.81: 62 Bond restraints: 13932 Sorted by residual: bond pdb=" C ARG H 152 " pdb=" N PRO H 153 " ideal model delta sigma weight residual 1.331 1.350 -0.019 1.27e-02 6.20e+03 2.22e+00 bond pdb=" C ARG F 152 " pdb=" N PRO F 153 " ideal model delta sigma weight residual 1.331 1.350 -0.019 1.27e-02 6.20e+03 2.22e+00 bond pdb=" CB VAL H 317 " pdb=" CG1 VAL H 317 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.56e+00 bond pdb=" CB VAL F 317 " pdb=" CG1 VAL F 317 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.56e+00 bond pdb=" CG LEU H 490 " pdb=" CD1 LEU H 490 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.41e+00 ... (remaining 13927 not shown) Histogram of bond angle deviations from ideal: 100.17 - 106.95: 800 106.95 - 113.72: 7687 113.72 - 120.50: 5364 120.50 - 127.27: 5048 127.27 - 134.05: 273 Bond angle restraints: 19172 Sorted by residual: angle pdb=" C PHE H 82 " pdb=" N ASP H 83 " pdb=" CA ASP H 83 " ideal model delta sigma weight residual 121.54 126.73 -5.19 1.91e+00 2.74e-01 7.37e+00 angle pdb=" C PHE F 82 " pdb=" N ASP F 83 " pdb=" CA ASP F 83 " ideal model delta sigma weight residual 121.54 126.66 -5.12 1.91e+00 2.74e-01 7.20e+00 angle pdb=" N ILE F 489 " pdb=" CA ILE F 489 " pdb=" C ILE F 489 " ideal model delta sigma weight residual 110.72 113.38 -2.66 1.01e+00 9.80e-01 6.93e+00 angle pdb=" N ILE H 489 " pdb=" CA ILE H 489 " pdb=" C ILE H 489 " ideal model delta sigma weight residual 110.72 113.34 -2.62 1.01e+00 9.80e-01 6.75e+00 angle pdb=" CA LYS G 302 " pdb=" CB LYS G 302 " pdb=" CG LYS G 302 " ideal model delta sigma weight residual 114.10 118.94 -4.84 2.00e+00 2.50e-01 5.85e+00 ... (remaining 19167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 7842 35.91 - 71.82: 218 71.82 - 107.74: 14 107.74 - 143.65: 0 143.65 - 179.56: 6 Dihedral angle restraints: 8080 sinusoidal: 3814 harmonic: 4266 Sorted by residual: dihedral pdb=" O4' U N 13 " pdb=" C1' U N 13 " pdb=" N1 U N 13 " pdb=" C2 U N 13 " ideal model delta sinusoidal sigma weight residual 200.00 20.44 179.56 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U A 13 " pdb=" C1' U A 13 " pdb=" N1 U A 13 " pdb=" C2 U A 13 " ideal model delta sinusoidal sigma weight residual 200.00 20.44 179.56 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U N 9 " pdb=" C1' U N 9 " pdb=" N1 U N 9 " pdb=" C2 U N 9 " ideal model delta sinusoidal sigma weight residual -160.00 -10.62 -149.38 1 1.50e+01 4.44e-03 7.94e+01 ... (remaining 8077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1409 0.033 - 0.067: 495 0.067 - 0.100: 131 0.100 - 0.133: 52 0.133 - 0.166: 5 Chirality restraints: 2092 Sorted by residual: chirality pdb=" CB ILE E 239 " pdb=" CA ILE E 239 " pdb=" CG1 ILE E 239 " pdb=" CG2 ILE E 239 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.93e-01 chirality pdb=" CB ILE G 239 " pdb=" CA ILE G 239 " pdb=" CG1 ILE G 239 " pdb=" CG2 ILE G 239 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.78e-01 chirality pdb=" CA ILE H 388 " pdb=" N ILE H 388 " pdb=" C ILE H 388 " pdb=" CB ILE H 388 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.94e-01 ... (remaining 2089 not shown) Planarity restraints: 2156 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS H 392 " 0.047 5.00e-02 4.00e+02 7.07e-02 8.00e+00 pdb=" N PRO H 393 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO H 393 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO H 393 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 392 " -0.046 5.00e-02 4.00e+02 7.06e-02 7.97e+00 pdb=" N PRO F 393 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO F 393 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO F 393 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 72 " 0.038 5.00e-02 4.00e+02 5.78e-02 5.34e+00 pdb=" N PRO F 73 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO F 73 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO F 73 " 0.032 5.00e-02 4.00e+02 ... (remaining 2153 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 351 2.68 - 3.24: 12584 3.24 - 3.79: 22295 3.79 - 4.35: 31171 4.35 - 4.90: 49036 Nonbonded interactions: 115437 Sorted by model distance: nonbonded pdb=" OE2 GLU E 284 " pdb=" OG1 THR E 291 " model vdw 2.128 2.440 nonbonded pdb=" OE2 GLU G 284 " pdb=" OG1 THR G 291 " model vdw 2.128 2.440 nonbonded pdb=" OH TYR G 221 " pdb=" O TYR G 233 " model vdw 2.224 2.440 nonbonded pdb=" OH TYR E 221 " pdb=" O TYR E 233 " model vdw 2.224 2.440 nonbonded pdb=" O LYS F 11 " pdb=" OG SER F 272 " model vdw 2.258 2.440 ... (remaining 115432 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 'N' } ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' } 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: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 6.480 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 39.320 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:17.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 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 : 0.003 0.041 13932 Z= 0.210 Angle : 0.548 5.757 19172 Z= 0.301 Chirality : 0.039 0.166 2092 Planarity : 0.005 0.071 2156 Dihedral : 16.349 179.559 5332 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.69 % Favored : 93.04 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.22), residues: 1436 helix: 0.86 (0.25), residues: 442 sheet: -0.64 (0.31), residues: 274 loop : -1.26 (0.22), residues: 720 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.447 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 193 average time/residue: 1.0063 time to fit residues: 216.9960 Evaluate side-chains 113 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 112 time to evaluate : 1.552 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2694 time to fit residues: 2.4608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 117 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 136 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 371 ASN F 307 ASN H 209 GLN ** H 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 344 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13932 Z= 0.241 Angle : 0.584 6.808 19172 Z= 0.308 Chirality : 0.042 0.223 2092 Planarity : 0.005 0.054 2156 Dihedral : 15.270 176.486 2380 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.64 % Favored : 94.08 % Rotamer: Outliers : 2.08 % Allowed : 8.64 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.22), residues: 1436 helix: 1.09 (0.25), residues: 448 sheet: -0.49 (0.32), residues: 268 loop : -1.32 (0.22), residues: 720 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 119 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 15 residues processed: 137 average time/residue: 1.1254 time to fit residues: 171.7440 Evaluate side-chains 119 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 104 time to evaluate : 1.491 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 10 residues processed: 6 average time/residue: 0.1589 time to fit residues: 3.6713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 chunk 147 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 135 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 307 ASN ** F 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 344 GLN ** H 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13932 Z= 0.217 Angle : 0.565 8.060 19172 Z= 0.296 Chirality : 0.041 0.144 2092 Planarity : 0.005 0.056 2156 Dihedral : 15.203 175.721 2380 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.36 % Favored : 94.36 % Rotamer: Outliers : 2.39 % Allowed : 10.96 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.22), residues: 1436 helix: 1.26 (0.25), residues: 436 sheet: -0.41 (0.33), residues: 272 loop : -1.23 (0.22), residues: 728 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 130 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 21 residues processed: 153 average time/residue: 0.9478 time to fit residues: 163.1467 Evaluate side-chains 136 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 115 time to evaluate : 1.069 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 18 residues processed: 4 average time/residue: 0.1433 time to fit residues: 2.6271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 15 optimal weight: 0.2980 chunk 65 optimal weight: 0.6980 chunk 91 optimal weight: 0.0060 chunk 136 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 129 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13932 Z= 0.171 Angle : 0.537 8.996 19172 Z= 0.284 Chirality : 0.040 0.158 2092 Planarity : 0.005 0.053 2156 Dihedral : 15.131 174.742 2380 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.29 % Favored : 94.43 % Rotamer: Outliers : 2.62 % Allowed : 11.88 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.22), residues: 1436 helix: 1.48 (0.25), residues: 436 sheet: -0.29 (0.33), residues: 272 loop : -1.17 (0.22), residues: 728 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 122 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 23 residues processed: 150 average time/residue: 1.0232 time to fit residues: 172.3879 Evaluate side-chains 134 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 111 time to evaluate : 1.429 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 19 residues processed: 6 average time/residue: 0.4195 time to fit residues: 5.0711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 8.9990 chunk 82 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 107 optimal weight: 0.3980 chunk 59 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 413 ASN ** H 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13932 Z= 0.194 Angle : 0.549 10.368 19172 Z= 0.286 Chirality : 0.040 0.146 2092 Planarity : 0.005 0.055 2156 Dihedral : 15.153 174.182 2380 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.43 % Favored : 94.29 % Rotamer: Outliers : 2.31 % Allowed : 13.04 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.22), residues: 1436 helix: 1.45 (0.25), residues: 436 sheet: -0.23 (0.34), residues: 272 loop : -1.09 (0.23), residues: 728 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 123 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 23 residues processed: 147 average time/residue: 1.0372 time to fit residues: 171.3067 Evaluate side-chains 134 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 111 time to evaluate : 1.354 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 19 residues processed: 5 average time/residue: 0.4791 time to fit residues: 4.9664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 120 optimal weight: 0.0980 chunk 67 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 139 optimal weight: 0.0870 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 307 ASN H 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13932 Z= 0.161 Angle : 0.535 12.251 19172 Z= 0.280 Chirality : 0.039 0.212 2092 Planarity : 0.005 0.052 2156 Dihedral : 15.101 173.455 2380 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.87 % Favored : 94.85 % Rotamer: Outliers : 1.93 % Allowed : 13.81 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.23), residues: 1436 helix: 1.55 (0.25), residues: 438 sheet: -0.03 (0.33), residues: 276 loop : -1.04 (0.23), residues: 722 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 122 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 21 residues processed: 143 average time/residue: 0.9558 time to fit residues: 154.6249 Evaluate side-chains 130 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 109 time to evaluate : 1.337 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 18 residues processed: 3 average time/residue: 0.1177 time to fit residues: 2.5224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 144 optimal weight: 0.3980 chunk 90 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 18 GLN F 307 ASN H 209 GLN ** H 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13932 Z= 0.297 Angle : 0.604 12.177 19172 Z= 0.312 Chirality : 0.042 0.141 2092 Planarity : 0.005 0.062 2156 Dihedral : 15.296 173.895 2380 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.99 % Favored : 93.73 % Rotamer: Outliers : 2.55 % Allowed : 13.97 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.22), residues: 1436 helix: 1.30 (0.25), residues: 436 sheet: -0.37 (0.33), residues: 280 loop : -1.14 (0.23), residues: 720 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 116 time to evaluate : 1.468 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 21 residues processed: 145 average time/residue: 1.0701 time to fit residues: 176.8930 Evaluate side-chains 130 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 109 time to evaluate : 1.206 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 18 residues processed: 3 average time/residue: 0.1440 time to fit residues: 2.8373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 28 optimal weight: 0.3980 chunk 91 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 131 optimal weight: 0.6980 chunk 138 optimal weight: 0.0970 chunk 126 optimal weight: 3.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 413 ASN F 307 ASN H 209 GLN ** H 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13932 Z= 0.178 Angle : 0.561 12.945 19172 Z= 0.290 Chirality : 0.040 0.175 2092 Planarity : 0.005 0.055 2156 Dihedral : 15.157 173.288 2380 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.08 % Favored : 94.64 % Rotamer: Outliers : 1.93 % Allowed : 15.20 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.23), residues: 1436 helix: 1.45 (0.25), residues: 436 sheet: 0.01 (0.34), residues: 260 loop : -1.07 (0.23), residues: 740 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 108 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 20 residues processed: 131 average time/residue: 0.9566 time to fit residues: 142.0990 Evaluate side-chains 125 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 105 time to evaluate : 1.272 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 19 residues processed: 2 average time/residue: 0.1844 time to fit residues: 2.4209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 127 optimal weight: 0.3980 chunk 88 optimal weight: 0.9990 chunk 142 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 59 HIS F 307 ASN ** H 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13932 Z= 0.238 Angle : 0.581 12.948 19172 Z= 0.300 Chirality : 0.041 0.152 2092 Planarity : 0.005 0.060 2156 Dihedral : 15.226 173.132 2380 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.71 % Favored : 94.01 % Rotamer: Outliers : 1.70 % Allowed : 15.28 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.22), residues: 1436 helix: 1.37 (0.25), residues: 436 sheet: -0.02 (0.34), residues: 260 loop : -1.13 (0.23), residues: 740 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 108 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 22 residues processed: 128 average time/residue: 0.9279 time to fit residues: 135.0172 Evaluate side-chains 129 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 107 time to evaluate : 1.461 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 20 residues processed: 3 average time/residue: 0.1639 time to fit residues: 2.7932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 chunk 137 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 72 optimal weight: 0.0980 chunk 94 optimal weight: 8.9990 chunk 126 optimal weight: 0.0970 chunk 36 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 307 ASN H 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13932 Z= 0.178 Angle : 0.557 12.634 19172 Z= 0.288 Chirality : 0.040 0.161 2092 Planarity : 0.005 0.055 2156 Dihedral : 15.130 172.439 2380 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.87 % Favored : 94.85 % Rotamer: Outliers : 1.62 % Allowed : 15.74 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.23), residues: 1436 helix: 1.50 (0.25), residues: 436 sheet: 0.00 (0.34), residues: 260 loop : -1.08 (0.23), residues: 740 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 114 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 22 residues processed: 133 average time/residue: 0.9542 time to fit residues: 143.6545 Evaluate side-chains 127 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 105 time to evaluate : 1.494 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 21 residues processed: 2 average time/residue: 0.1668 time to fit residues: 2.5843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 0.7980 chunk 17 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 49 optimal weight: 0.0870 chunk 122 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 307 ASN ** F 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.195654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.159649 restraints weight = 16499.428| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 2.43 r_work: 0.3804 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13932 Z= 0.194 Angle : 0.565 11.813 19172 Z= 0.291 Chirality : 0.040 0.144 2092 Planarity : 0.005 0.058 2156 Dihedral : 15.139 172.152 2380 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.57 % Favored : 94.15 % Rotamer: Outliers : 1.62 % Allowed : 15.97 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.23), residues: 1436 helix: 1.50 (0.25), residues: 436 sheet: 0.01 (0.35), residues: 260 loop : -1.09 (0.23), residues: 740 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3757.00 seconds wall clock time: 73 minutes 44.56 seconds (4424.56 seconds total)