Starting phenix.real_space_refine (version: dev) on Fri Feb 17 13:48:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gsz_34244/02_2023/8gsz_34244.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gsz_34244/02_2023/8gsz_34244.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gsz_34244/02_2023/8gsz_34244.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gsz_34244/02_2023/8gsz_34244.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gsz_34244/02_2023/8gsz_34244.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gsz_34244/02_2023/8gsz_34244.pdb" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.000 sd= 0.003 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 140 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ARG 14": "NH1" <-> "NH2" Residue "A GLU 38": "OE1" <-> "OE2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "B ARG 14": "NH1" <-> "NH2" Residue "B GLU 38": "OE1" <-> "OE2" Residue "B GLU 282": "OE1" <-> "OE2" Residue "B GLU 316": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 4870 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2435 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 295} Chain breaks: 5 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 2435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2435 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 295} Chain breaks: 5 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 2.95, per 1000 atoms: 0.61 Number of scatterers: 4870 At special positions: 0 Unit cell: (84.609, 73.899, 106.029, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 872 8.00 N 854 7.00 C 3118 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: 1.68 Conformation dependent library (CDL) restraints added in 597.7 milliseconds 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1160 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 2 sheets defined 62.3% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 16 through 31 removed outlier: 3.551A pdb=" N ALA A 21 " --> pdb=" O GLY A 17 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 23 " --> pdb=" O GLN A 19 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL A 24 " --> pdb=" O LYS A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 38 removed outlier: 3.678A pdb=" N GLU A 38 " --> pdb=" O TRP A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 65 removed outlier: 3.593A pdb=" N VAL A 48 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY A 57 " --> pdb=" O SER A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 72 removed outlier: 4.025A pdb=" N ARG A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N HIS A 72 " --> pdb=" O GLU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 78 Processing helix chain 'A' and resid 80 through 90 removed outlier: 3.844A pdb=" N THR A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 108 removed outlier: 4.134A pdb=" N ARG A 95 " --> pdb=" O CYS A 91 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU A 98 " --> pdb=" O ARG A 94 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 134 removed outlier: 4.115A pdb=" N LEU A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A 132 " --> pdb=" O GLN A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 151 removed outlier: 3.505A pdb=" N LEU A 147 " --> pdb=" O GLU A 143 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 167 removed outlier: 3.590A pdb=" N SER A 162 " --> pdb=" O GLY A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 186 removed outlier: 3.655A pdb=" N ARG A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR A 186 " --> pdb=" O TYR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 273 removed outlier: 3.717A pdb=" N GLN A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR A 267 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 288 removed outlier: 3.643A pdb=" N ALA A 288 " --> pdb=" O ARG A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 302 removed outlier: 3.978A pdb=" N GLU A 296 " --> pdb=" O CYS A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 307 removed outlier: 3.719A pdb=" N GLN A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN A 307 " --> pdb=" O PRO A 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 302 through 307' Processing helix chain 'A' and resid 324 through 335 removed outlier: 4.250A pdb=" N GLU A 328 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN A 335 " --> pdb=" O ARG A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 31 removed outlier: 3.551A pdb=" N ALA B 21 " --> pdb=" O GLY B 17 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B 23 " --> pdb=" O GLN B 19 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL B 24 " --> pdb=" O LYS B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 38 removed outlier: 3.678A pdb=" N GLU B 38 " --> pdb=" O TRP B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 65 removed outlier: 3.593A pdb=" N VAL B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY B 57 " --> pdb=" O SER B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 72 removed outlier: 4.025A pdb=" N ARG B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N HIS B 72 " --> pdb=" O GLU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 78 Processing helix chain 'B' and resid 80 through 90 removed outlier: 3.844A pdb=" N THR B 84 " --> pdb=" O SER B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 108 removed outlier: 4.134A pdb=" N ARG B 95 " --> pdb=" O CYS B 91 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU B 98 " --> pdb=" O ARG B 94 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 134 removed outlier: 4.115A pdb=" N LEU B 124 " --> pdb=" O MET B 120 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE B 132 " --> pdb=" O GLN B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 151 removed outlier: 3.505A pdb=" N LEU B 147 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 167 removed outlier: 3.590A pdb=" N SER B 162 " --> pdb=" O GLY B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.655A pdb=" N ARG B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR B 186 " --> pdb=" O TYR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 273 removed outlier: 3.717A pdb=" N GLN B 266 " --> pdb=" O ALA B 262 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 288 removed outlier: 3.643A pdb=" N ALA B 288 " --> pdb=" O ARG B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 302 removed outlier: 3.978A pdb=" N GLU B 296 " --> pdb=" O CYS B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 307 removed outlier: 3.719A pdb=" N GLN B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN B 307 " --> pdb=" O PRO B 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 302 through 307' Processing helix chain 'B' and resid 324 through 335 removed outlier: 4.250A pdb=" N GLU B 328 " --> pdb=" O SER B 324 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN B 335 " --> pdb=" O ARG B 331 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 244 through 249 removed outlier: 3.691A pdb=" N GLY A 255 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLU A 249 " --> pdb=" O ARG A 253 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ARG A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU A 198 " --> pdb=" O ARG A 310 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ILE A 312 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE A 200 " --> pdb=" O ILE A 312 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 244 through 249 removed outlier: 3.691A pdb=" N GLY B 255 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLU B 249 " --> pdb=" O ARG B 253 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ARG B 253 " --> pdb=" O GLU B 249 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU B 198 " --> pdb=" O ARG B 310 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ILE B 312 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE B 200 " --> pdb=" O ILE B 312 " (cutoff:3.500A) 204 hydrogen bonds defined for protein. 612 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: 0.99 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1588 1.34 - 1.46: 1126 1.46 - 1.58: 2226 1.58 - 1.70: 0 1.70 - 1.81: 32 Bond restraints: 4972 Sorted by residual: bond pdb=" N VAL A 194 " pdb=" CA VAL A 194 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.18e-02 7.18e+03 9.66e+00 bond pdb=" N VAL B 194 " pdb=" CA VAL B 194 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.18e-02 7.18e+03 9.66e+00 bond pdb=" N HIS B 72 " pdb=" CA HIS B 72 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.18e-02 7.18e+03 8.92e+00 bond pdb=" N HIS A 72 " pdb=" CA HIS A 72 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.18e-02 7.18e+03 8.92e+00 bond pdb=" N ILE A 73 " pdb=" CA ILE A 73 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.70e+00 ... (remaining 4967 not shown) Histogram of bond angle deviations from ideal: 99.94 - 106.77: 146 106.77 - 113.60: 2708 113.60 - 120.43: 2086 120.43 - 127.26: 1742 127.26 - 134.09: 58 Bond angle restraints: 6740 Sorted by residual: angle pdb=" C TYR A 77 " pdb=" N ARG A 78 " pdb=" CA ARG A 78 " ideal model delta sigma weight residual 122.08 127.51 -5.43 1.47e+00 4.63e-01 1.37e+01 angle pdb=" C TYR B 77 " pdb=" N ARG B 78 " pdb=" CA ARG B 78 " ideal model delta sigma weight residual 122.08 127.51 -5.43 1.47e+00 4.63e-01 1.37e+01 angle pdb=" C GLU B 249 " pdb=" N ASN B 250 " pdb=" CA ASN B 250 " ideal model delta sigma weight residual 122.46 127.15 -4.69 1.41e+00 5.03e-01 1.11e+01 angle pdb=" C GLU A 249 " pdb=" N ASN A 250 " pdb=" CA ASN A 250 " ideal model delta sigma weight residual 122.46 127.15 -4.69 1.41e+00 5.03e-01 1.11e+01 angle pdb=" CA ILE B 73 " pdb=" C ILE B 73 " pdb=" O ILE B 73 " ideal model delta sigma weight residual 120.95 117.51 3.44 1.04e+00 9.25e-01 1.09e+01 ... (remaining 6735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.97: 2532 14.97 - 29.95: 302 29.95 - 44.92: 106 44.92 - 59.89: 12 59.89 - 74.86: 14 Dihedral angle restraints: 2966 sinusoidal: 1164 harmonic: 1802 Sorted by residual: dihedral pdb=" CA ASN B 154 " pdb=" C ASN B 154 " pdb=" N VAL B 155 " pdb=" CA VAL B 155 " ideal model delta harmonic sigma weight residual -180.00 -150.27 -29.73 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA ASN A 154 " pdb=" C ASN A 154 " pdb=" N VAL A 155 " pdb=" CA VAL A 155 " ideal model delta harmonic sigma weight residual -180.00 -150.27 -29.73 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA GLU B 328 " pdb=" C GLU B 328 " pdb=" N VAL B 329 " pdb=" CA VAL B 329 " ideal model delta harmonic sigma weight residual 180.00 162.01 17.99 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 2963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 442 0.040 - 0.079: 242 0.079 - 0.118: 54 0.118 - 0.158: 16 0.158 - 0.197: 8 Chirality restraints: 762 Sorted by residual: chirality pdb=" CA LEU A 198 " pdb=" N LEU A 198 " pdb=" C LEU A 198 " pdb=" CB LEU A 198 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.73e-01 chirality pdb=" CA LEU B 198 " pdb=" N LEU B 198 " pdb=" C LEU B 198 " pdb=" CB LEU B 198 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.73e-01 chirality pdb=" CA ARG B 71 " pdb=" N ARG B 71 " pdb=" C ARG B 71 " pdb=" CB ARG B 71 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.71e-01 ... (remaining 759 not shown) Planarity restraints: 854 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 263 " -0.042 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO B 264 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 264 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 264 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 263 " 0.042 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO A 264 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 264 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 264 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 172 " 0.036 5.00e-02 4.00e+02 5.32e-02 4.53e+00 pdb=" N PRO B 173 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 173 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 173 " 0.030 5.00e-02 4.00e+02 ... (remaining 851 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1064 2.77 - 3.30: 4390 3.30 - 3.84: 7845 3.84 - 4.37: 9309 4.37 - 4.90: 15438 Nonbonded interactions: 38046 Sorted by model distance: nonbonded pdb=" NH2 ARG A 197 " pdb=" CG ARG A 310 " model vdw 2.241 3.520 nonbonded pdb=" NH2 ARG B 197 " pdb=" CG ARG B 310 " model vdw 2.241 3.520 nonbonded pdb=" OE1 GLU B 246 " pdb=" OG1 THR B 256 " model vdw 2.279 2.440 nonbonded pdb=" OE1 GLU A 246 " pdb=" OG1 THR A 256 " model vdw 2.279 2.440 nonbonded pdb=" O LEU B 99 " pdb=" OG SER B 102 " model vdw 2.365 2.440 ... (remaining 38041 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 3118 2.51 5 N 854 2.21 5 O 872 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 4.350 Check model and map are aligned: 0.070 Process input model: 14.730 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.050 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 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 : 0.006 0.099 4972 Z= 0.373 Angle : 0.862 7.903 6740 Z= 0.489 Chirality : 0.051 0.197 762 Planarity : 0.006 0.063 854 Dihedral : 15.613 74.864 1806 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 0.39 % 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: -5.38 (0.24), residues: 596 helix: -4.27 (0.12), residues: 348 sheet: -2.93 (0.62), residues: 36 loop : -1.91 (0.38), residues: 212 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 162 time to evaluate : 0.637 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 164 average time/residue: 0.1875 time to fit residues: 38.1701 Evaluate side-chains 112 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.576 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 0.0270 chunk 25 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 0.0470 chunk 36 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 overall best weight: 0.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 HIS A 61 ASN A 74 HIS A 131 ASN A 154 ASN A 157 HIS A 218 ASN A 273 GLN A 307 ASN B 7 HIS B 61 ASN B 74 HIS B 131 ASN B 154 ASN B 157 HIS B 218 ASN B 273 GLN B 307 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 4972 Z= 0.162 Angle : 0.610 6.035 6740 Z= 0.300 Chirality : 0.040 0.120 762 Planarity : 0.004 0.040 854 Dihedral : 4.824 25.123 684 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 1.94 % 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: -3.58 (0.29), residues: 596 helix: -2.49 (0.21), residues: 364 sheet: -2.02 (0.61), residues: 54 loop : -1.64 (0.44), residues: 178 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 126 time to evaluate : 0.605 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 130 average time/residue: 0.1423 time to fit residues: 24.5987 Evaluate side-chains 126 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 122 time to evaluate : 0.475 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0519 time to fit residues: 1.1446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS A 61 ASN A 72 HIS B 3 HIS B 61 ASN B 72 HIS B 154 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 4972 Z= 0.252 Angle : 0.634 5.879 6740 Z= 0.306 Chirality : 0.041 0.124 762 Planarity : 0.004 0.036 854 Dihedral : 4.684 25.482 684 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer Outliers : 4.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.32), residues: 596 helix: -1.68 (0.25), residues: 370 sheet: -2.08 (0.62), residues: 54 loop : -1.63 (0.46), residues: 172 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 100 time to evaluate : 0.540 Fit side-chains outliers start: 24 outliers final: 10 residues processed: 118 average time/residue: 0.1584 time to fit residues: 24.5188 Evaluate side-chains 106 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 96 time to evaluate : 0.577 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0534 time to fit residues: 1.6971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 0.0970 chunk 42 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 0.0970 chunk 56 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 53 optimal weight: 0.0770 chunk 16 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 overall best weight: 0.2934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS A 72 HIS B 3 HIS B 72 HIS B 154 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 4972 Z= 0.130 Angle : 0.591 8.633 6740 Z= 0.267 Chirality : 0.038 0.115 762 Planarity : 0.003 0.031 854 Dihedral : 4.167 21.911 684 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer Outliers : 2.71 % 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: -2.09 (0.33), residues: 596 helix: -0.88 (0.26), residues: 374 sheet: -2.47 (0.74), residues: 42 loop : -1.84 (0.44), residues: 180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 138 time to evaluate : 0.597 Fit side-chains outliers start: 14 outliers final: 14 residues processed: 144 average time/residue: 0.1667 time to fit residues: 30.7211 Evaluate side-chains 128 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 0.601 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0503 time to fit residues: 2.0280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 51 optimal weight: 0.0030 chunk 41 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 15 optimal weight: 0.2980 chunk 20 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 HIS B 3 HIS B 72 HIS B 154 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 4972 Z= 0.166 Angle : 0.610 7.428 6740 Z= 0.279 Chirality : 0.040 0.142 762 Planarity : 0.003 0.029 854 Dihedral : 4.127 22.065 684 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer Outliers : 2.71 % 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: -1.52 (0.34), residues: 596 helix: -0.51 (0.27), residues: 374 sheet: -1.72 (1.12), residues: 22 loop : -1.67 (0.41), residues: 200 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 126 time to evaluate : 0.572 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 134 average time/residue: 0.1510 time to fit residues: 26.4284 Evaluate side-chains 130 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 122 time to evaluate : 0.578 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1146 time to fit residues: 2.0230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS A 72 HIS A 154 ASN B 3 HIS B 72 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 4972 Z= 0.216 Angle : 0.627 7.267 6740 Z= 0.293 Chirality : 0.041 0.118 762 Planarity : 0.004 0.046 854 Dihedral : 4.239 23.129 684 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 2.33 % 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: -1.36 (0.34), residues: 596 helix: -0.25 (0.27), residues: 374 sheet: -2.22 (0.61), residues: 48 loop : -1.66 (0.46), residues: 174 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 122 time to evaluate : 0.580 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 128 average time/residue: 0.1603 time to fit residues: 26.7488 Evaluate side-chains 120 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 114 time to evaluate : 0.575 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0523 time to fit residues: 1.3544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS B 72 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 4972 Z= 0.212 Angle : 0.617 7.373 6740 Z= 0.289 Chirality : 0.041 0.119 762 Planarity : 0.003 0.032 854 Dihedral : 4.230 23.150 684 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer Outliers : 1.55 % 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: -1.21 (0.34), residues: 596 helix: -0.13 (0.27), residues: 374 sheet: -2.30 (0.58), residues: 48 loop : -1.57 (0.46), residues: 174 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 126 time to evaluate : 0.619 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 130 average time/residue: 0.1460 time to fit residues: 25.5010 Evaluate side-chains 118 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 0.763 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0503 time to fit residues: 0.9758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 57 optimal weight: 0.0870 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS B 72 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 4972 Z= 0.173 Angle : 0.591 7.386 6740 Z= 0.275 Chirality : 0.040 0.114 762 Planarity : 0.003 0.031 854 Dihedral : 4.137 22.426 684 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.35), residues: 596 helix: 0.14 (0.28), residues: 376 sheet: -2.29 (0.57), residues: 48 loop : -1.35 (0.48), residues: 172 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 126 time to evaluate : 0.592 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 130 average time/residue: 0.1548 time to fit residues: 26.5147 Evaluate side-chains 120 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 118 time to evaluate : 0.594 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0527 time to fit residues: 0.9886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 50 optimal weight: 0.0570 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS B 72 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 4972 Z= 0.202 Angle : 0.614 7.382 6740 Z= 0.292 Chirality : 0.041 0.124 762 Planarity : 0.003 0.032 854 Dihedral : 4.215 22.819 684 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.35), residues: 596 helix: 0.09 (0.28), residues: 374 sheet: -2.34 (0.54), residues: 48 loop : -1.36 (0.48), residues: 174 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 120 time to evaluate : 0.596 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 122 average time/residue: 0.1529 time to fit residues: 25.1657 Evaluate side-chains 118 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 0.602 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0555 time to fit residues: 1.0217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 49 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS B 72 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 4972 Z= 0.177 Angle : 0.630 7.841 6740 Z= 0.301 Chirality : 0.040 0.191 762 Planarity : 0.004 0.031 854 Dihedral : 4.181 22.217 684 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.35), residues: 596 helix: 0.19 (0.28), residues: 376 sheet: -2.54 (0.68), residues: 36 loop : -1.23 (0.46), residues: 184 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 122 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 124 average time/residue: 0.1688 time to fit residues: 26.9502 Evaluate side-chains 116 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 112 time to evaluate : 0.542 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0545 time to fit residues: 1.1874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 50 optimal weight: 0.2980 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 43 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS B 72 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.156684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.127971 restraints weight = 7920.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.131485 restraints weight = 4952.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.133691 restraints weight = 3697.745| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 4972 Z= 0.174 Angle : 0.617 7.757 6740 Z= 0.297 Chirality : 0.040 0.165 762 Planarity : 0.003 0.031 854 Dihedral : 4.127 21.724 684 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.35), residues: 596 helix: 0.20 (0.28), residues: 376 sheet: -2.62 (0.66), residues: 36 loop : -1.16 (0.47), residues: 184 =============================================================================== Job complete usr+sys time: 1341.12 seconds wall clock time: 24 minutes 49.73 seconds (1489.73 seconds total)