Starting phenix.real_space_refine (version: dev) on Fri Feb 17 17:07:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hc8_34655/02_2023/8hc8_34655.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hc8_34655/02_2023/8hc8_34655.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hc8_34655/02_2023/8hc8_34655.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hc8_34655/02_2023/8hc8_34655.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hc8_34655/02_2023/8hc8_34655.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hc8_34655/02_2023/8hc8_34655.pdb" } resolution = 3.95 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= 0.086 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 809 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 "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 39": "OD1" <-> "OD2" Residue "L ASP 65": "OD1" <-> "OD2" Residue "L PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 148": "OE1" <-> "OE2" Residue "L GLU 166": "OE1" <-> "OE2" Residue "L GLU 170": "OE1" <-> "OE2" Residue "L GLU 200": "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: 4832 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1508 Classifications: {'peptide': 186} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 175} Chain: "H" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1734 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 220} Chain: "L" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1576 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 13, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.25, per 1000 atoms: 0.67 Number of scatterers: 4832 At special positions: 0 Unit cell: (80.85, 90.75, 113.85, 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 22 16.00 O 943 8.00 N 811 7.00 C 3056 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 100 " distance=2.03 Simple disulfide: pdb=" SG CYS H 111 " - pdb=" SG CYS H 116 " distance=2.03 Simple disulfide: pdb=" SG CYS H 161 " - pdb=" SG CYS H 217 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.04 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 Links applied NAG-ASN " NAG C 601 " - " ASN C 343 " Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 743.4 milliseconds 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1166 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 14 sheets defined 7.0% alpha, 30.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.833A pdb=" N LEU C 368 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 370' Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.526A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.885A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'H' and resid 78 through 80 No H-bonds generated for 'chain 'H' and resid 78 through 80' Processing helix chain 'H' and resid 177 through 179 No H-bonds generated for 'chain 'H' and resid 177 through 179' Processing helix chain 'H' and resid 208 through 210 No H-bonds generated for 'chain 'H' and resid 208 through 210' Processing helix chain 'L' and resid 126 through 131 removed outlier: 3.753A pdb=" N LYS L 131 " --> pdb=" O ASP L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 188 through 193 removed outlier: 3.679A pdb=" N LYS L 193 " --> pdb=" O ALA L 189 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.727A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'C' and resid 473 through 474 removed outlier: 4.244A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.508A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER H 7 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU H 20 " --> pdb=" O LEU H 85 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER H 82 " --> pdb=" O ASP H 77 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER H 75 " --> pdb=" O PHE H 84 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N THR H 73 " --> pdb=" O GLN H 86 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.563A pdb=" N TYR H 98 " --> pdb=" O THR H 128 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL H 130 " --> pdb=" O ALA H 96 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA H 96 " --> pdb=" O VAL H 130 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN H 35 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.563A pdb=" N TYR H 98 " --> pdb=" O THR H 128 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL H 130 " --> pdb=" O ALA H 96 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA H 96 " --> pdb=" O VAL H 130 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG H 102 " --> pdb=" O LEU H 123 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU H 123 " --> pdb=" O ARG H 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 141 through 144 removed outlier: 3.546A pdb=" N SER H 141 " --> pdb=" O LYS H 164 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU H 162 " --> pdb=" O PHE H 143 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL H 205 " --> pdb=" O ALA H 157 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU H 159 " --> pdb=" O VAL H 203 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP H 165 " --> pdb=" O TYR H 197 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TYR H 197 " --> pdb=" O ASP H 165 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL H 202 " --> pdb=" O HIS H 185 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N HIS H 185 " --> pdb=" O VAL H 202 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 141 through 144 removed outlier: 3.546A pdb=" N SER H 141 " --> pdb=" O LYS H 164 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU H 162 " --> pdb=" O PHE H 143 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL H 205 " --> pdb=" O ALA H 157 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU H 159 " --> pdb=" O VAL H 203 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP H 165 " --> pdb=" O TYR H 197 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TYR H 197 " --> pdb=" O ASP H 165 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N SER H 198 " --> pdb=" O VAL H 190 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL H 190 " --> pdb=" O SER H 198 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 172 through 175 removed outlier: 3.706A pdb=" N CYS H 217 " --> pdb=" O LYS H 230 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS H 230 " --> pdb=" O CYS H 217 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL H 219 " --> pdb=" O VAL H 228 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL H 228 " --> pdb=" O VAL H 219 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N HIS H 221 " --> pdb=" O THR H 226 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR H 226 " --> pdb=" O HIS H 221 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.897A pdb=" N CYS L 23 " --> pdb=" O PHE L 76 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE L 76 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER L 70 " --> pdb=" O THR L 77 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 12 through 13 Processing sheet with id=AB3, first strand: chain 'L' and resid 50 through 53 removed outlier: 5.748A pdb=" N LEU L 51 " --> pdb=" O LEU L 42 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU L 42 " --> pdb=" O LEU L 51 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE L 53 " --> pdb=" O TRP L 40 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL L 90 " --> pdb=" O GLN L 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 121 through 123 removed outlier: 3.555A pdb=" N PHE L 123 " --> pdb=" O VAL L 138 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER L 182 " --> pdb=" O CYS L 139 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 152 through 155 removed outlier: 3.861A pdb=" N GLN L 152 " --> pdb=" O GLU L 200 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS L 212 " --> pdb=" O CYS L 199 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL L 201 " --> pdb=" O VAL L 210 " (cutoff:3.500A) 92 hydrogen bonds defined for protein. 237 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: 1.29 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1552 1.35 - 1.46: 1248 1.46 - 1.58: 2124 1.58 - 1.70: 0 1.70 - 1.82: 26 Bond restraints: 4950 Sorted by residual: bond pdb=" C ALA C 372 " pdb=" N PRO C 373 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.23e+00 bond pdb=" C SER L 7 " pdb=" N PRO L 8 " ideal model delta sigma weight residual 1.334 1.371 -0.037 2.34e-02 1.83e+03 2.47e+00 bond pdb=" CB PRO H 144 " pdb=" CG PRO H 144 " ideal model delta sigma weight residual 1.492 1.562 -0.070 5.00e-02 4.00e+02 1.96e+00 bond pdb=" CB GLU L 200 " pdb=" CG GLU L 200 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.73e+00 bond pdb=" C PHE H 187 " pdb=" N PRO H 188 " ideal model delta sigma weight residual 1.328 1.344 -0.016 1.26e-02 6.30e+03 1.57e+00 ... (remaining 4945 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.13: 158 107.13 - 113.83: 2657 113.83 - 120.54: 1824 120.54 - 127.24: 2051 127.24 - 133.94: 53 Bond angle restraints: 6743 Sorted by residual: angle pdb=" C TYR L 145 " pdb=" N PRO L 146 " pdb=" CA PRO L 146 " ideal model delta sigma weight residual 119.84 115.17 4.67 1.25e+00 6.40e-01 1.39e+01 angle pdb=" C PHE C 377 " pdb=" N LYS C 378 " pdb=" CA LYS C 378 " ideal model delta sigma weight residual 122.46 127.37 -4.91 1.41e+00 5.03e-01 1.21e+01 angle pdb=" CA PRO H 144 " pdb=" N PRO H 144 " pdb=" CD PRO H 144 " ideal model delta sigma weight residual 112.00 107.57 4.43 1.40e+00 5.10e-01 1.00e+01 angle pdb=" C SER C 359 " pdb=" N ASN C 360 " pdb=" CA ASN C 360 " ideal model delta sigma weight residual 122.46 126.85 -4.39 1.41e+00 5.03e-01 9.69e+00 angle pdb=" N ILE L 111 " pdb=" CA ILE L 111 " pdb=" C ILE L 111 " ideal model delta sigma weight residual 109.12 113.87 -4.75 1.58e+00 4.01e-01 9.05e+00 ... (remaining 6738 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 2505 17.19 - 34.39: 330 34.39 - 51.58: 97 51.58 - 68.77: 10 68.77 - 85.97: 5 Dihedral angle restraints: 2947 sinusoidal: 1122 harmonic: 1825 Sorted by residual: dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual -86.00 -32.64 -53.36 1 1.00e+01 1.00e-02 3.87e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 100 " pdb=" CB CYS H 100 " ideal model delta sinusoidal sigma weight residual -86.00 -126.30 40.30 1 1.00e+01 1.00e-02 2.28e+01 dihedral pdb=" CA LEU L 141 " pdb=" C LEU L 141 " pdb=" N ASN L 142 " pdb=" CA ASN L 142 " ideal model delta harmonic sigma weight residual -180.00 -162.58 -17.42 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 2944 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 483 0.037 - 0.074: 183 0.074 - 0.111: 69 0.111 - 0.148: 14 0.148 - 0.185: 5 Chirality restraints: 754 Sorted by residual: chirality pdb=" CA THR L 99 " pdb=" N THR L 99 " pdb=" C THR L 99 " pdb=" CB THR L 99 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.52e-01 chirality pdb=" CG LEU L 186 " pdb=" CB LEU L 186 " pdb=" CD1 LEU L 186 " pdb=" CD2 LEU L 186 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.13e-01 chirality pdb=" CB ILE H 216 " pdb=" CA ILE H 216 " pdb=" CG1 ILE H 216 " pdb=" CG2 ILE H 216 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.25e-01 ... (remaining 751 not shown) Planarity restraints: 872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER H 134 " 0.027 2.00e-02 2.50e+03 5.30e-02 2.81e+01 pdb=" C SER H 134 " -0.092 2.00e-02 2.50e+03 pdb=" O SER H 134 " 0.034 2.00e-02 2.50e+03 pdb=" N ALA H 135 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE H 143 " -0.082 5.00e-02 4.00e+02 1.22e-01 2.39e+01 pdb=" N PRO H 144 " 0.211 5.00e-02 4.00e+02 pdb=" CA PRO H 144 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO H 144 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 369 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C TYR C 369 " 0.056 2.00e-02 2.50e+03 pdb=" O TYR C 369 " -0.021 2.00e-02 2.50e+03 pdb=" N ASN C 370 " -0.019 2.00e-02 2.50e+03 ... (remaining 869 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 1580 2.83 - 3.35: 3756 3.35 - 3.87: 7648 3.87 - 4.38: 7956 4.38 - 4.90: 14303 Nonbonded interactions: 35243 Sorted by model distance: nonbonded pdb=" OG1 THR C 430 " pdb=" O PHE C 515 " model vdw 2.317 2.440 nonbonded pdb=" OG SER L 70 " pdb=" O THR L 77 " model vdw 2.371 2.440 nonbonded pdb=" OG SER L 187 " pdb=" OD2 ASP L 190 " model vdw 2.375 2.440 nonbonded pdb=" OH TYR H 63 " pdb=" O THR H 112 " model vdw 2.410 2.440 nonbonded pdb=" N ASN C 354 " pdb=" OD1 ASN C 354 " model vdw 2.415 2.520 ... (remaining 35238 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 22 5.16 5 C 3056 2.51 5 N 811 2.21 5 O 943 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 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: 0.010 Extract box with map and model: 4.430 Check model and map are aligned: 0.070 Process input model: 16.700 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.040 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 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 0.070 4950 Z= 0.200 Angle : 0.708 9.829 6743 Z= 0.362 Chirality : 0.046 0.185 754 Planarity : 0.007 0.122 871 Dihedral : 16.631 85.966 1757 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.32), residues: 620 helix: -4.33 (0.50), residues: 20 sheet: 1.02 (0.43), residues: 161 loop : -1.42 (0.27), residues: 439 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 79 time to evaluate : 0.590 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 82 average time/residue: 0.1508 time to fit residues: 16.4863 Evaluate side-chains 73 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 0.540 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0447 time to fit residues: 0.8182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 31 optimal weight: 0.3980 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 185 HIS H 218 ASN L 36 ASN L 129 GLN L 194 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 4950 Z= 0.344 Angle : 0.655 9.235 6743 Z= 0.333 Chirality : 0.045 0.167 754 Planarity : 0.006 0.081 871 Dihedral : 4.207 20.854 692 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer Outliers : 6.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.33 (0.32), residues: 620 helix: -4.31 (0.48), residues: 35 sheet: 0.83 (0.42), residues: 162 loop : -1.36 (0.28), residues: 423 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 75 time to evaluate : 0.580 Fit side-chains outliers start: 33 outliers final: 21 residues processed: 102 average time/residue: 0.1598 time to fit residues: 21.3018 Evaluate side-chains 90 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 69 time to evaluate : 0.575 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.0694 time to fit residues: 3.0436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 0.0980 chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 33 ASN H 218 ASN ** L 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 4950 Z= 0.180 Angle : 0.533 6.562 6743 Z= 0.265 Chirality : 0.043 0.140 754 Planarity : 0.004 0.065 871 Dihedral : 3.710 18.314 692 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer Outliers : 2.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.32), residues: 620 helix: -4.10 (0.58), residues: 34 sheet: 0.77 (0.41), residues: 162 loop : -1.24 (0.28), residues: 424 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 79 time to evaluate : 0.532 Fit side-chains outliers start: 16 outliers final: 6 residues processed: 89 average time/residue: 0.1589 time to fit residues: 18.6884 Evaluate side-chains 75 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 0.599 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0510 time to fit residues: 1.3192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 0.0970 chunk 15 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 218 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 4950 Z= 0.339 Angle : 0.645 8.172 6743 Z= 0.327 Chirality : 0.045 0.180 754 Planarity : 0.005 0.057 871 Dihedral : 4.418 19.708 692 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer Outliers : 3.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.53 (0.32), residues: 620 helix: -4.09 (0.50), residues: 43 sheet: 0.46 (0.41), residues: 172 loop : -1.40 (0.28), residues: 405 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 79 time to evaluate : 0.635 Fit side-chains outliers start: 21 outliers final: 10 residues processed: 94 average time/residue: 0.1804 time to fit residues: 21.6372 Evaluate side-chains 83 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 0.588 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0480 time to fit residues: 1.6751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 0.2980 chunk 30 optimal weight: 0.9980 chunk 52 optimal weight: 0.0170 chunk 14 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 overall best weight: 1.0420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 33 ASN H 218 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 4950 Z= 0.238 Angle : 0.572 7.702 6743 Z= 0.287 Chirality : 0.044 0.171 754 Planarity : 0.004 0.051 871 Dihedral : 4.109 18.848 692 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer Outliers : 3.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.49 (0.32), residues: 620 helix: -3.84 (0.59), residues: 37 sheet: 0.42 (0.41), residues: 170 loop : -1.40 (0.28), residues: 413 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 76 time to evaluate : 0.518 Fit side-chains outliers start: 21 outliers final: 9 residues processed: 91 average time/residue: 0.1932 time to fit residues: 22.1712 Evaluate side-chains 79 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 0.549 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0789 time to fit residues: 1.8134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 6 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 218 ASN L 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 4950 Z= 0.248 Angle : 0.582 7.956 6743 Z= 0.292 Chirality : 0.044 0.189 754 Planarity : 0.004 0.048 871 Dihedral : 4.154 19.956 692 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer Outliers : 3.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.55 (0.32), residues: 620 helix: -3.75 (0.59), residues: 37 sheet: 0.29 (0.40), residues: 170 loop : -1.41 (0.28), residues: 413 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 77 time to evaluate : 0.590 Fit side-chains outliers start: 19 outliers final: 7 residues processed: 88 average time/residue: 0.2041 time to fit residues: 22.9067 Evaluate side-chains 79 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 0.586 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0494 time to fit residues: 1.4296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 40.0000 chunk 43 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 58 optimal weight: 0.0970 chunk 36 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 17 optimal weight: 4.9990 chunk 11 optimal weight: 0.0470 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 218 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 4950 Z= 0.158 Angle : 0.543 7.414 6743 Z= 0.269 Chirality : 0.043 0.197 754 Planarity : 0.004 0.046 871 Dihedral : 3.867 18.784 692 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.46 (0.32), residues: 620 helix: -3.64 (0.66), residues: 34 sheet: 0.31 (0.40), residues: 172 loop : -1.37 (0.28), residues: 414 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 74 time to evaluate : 0.593 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 80 average time/residue: 0.1939 time to fit residues: 19.8031 Evaluate side-chains 72 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 0.635 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0719 time to fit residues: 1.0710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.0040 chunk 37 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 5 optimal weight: 0.0040 chunk 46 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 overall best weight: 0.5004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 185 HIS H 218 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 4950 Z= 0.163 Angle : 0.541 7.331 6743 Z= 0.268 Chirality : 0.043 0.206 754 Planarity : 0.004 0.046 871 Dihedral : 3.807 19.089 692 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.43 (0.32), residues: 620 helix: -3.59 (0.66), residues: 34 sheet: 0.31 (0.40), residues: 171 loop : -1.33 (0.28), residues: 415 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 0.581 Fit side-chains outliers start: 7 outliers final: 0 residues processed: 78 average time/residue: 0.1973 time to fit residues: 19.4666 Evaluate side-chains 70 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.631 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 0.2980 chunk 43 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 185 HIS H 218 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 4950 Z= 0.197 Angle : 0.555 7.836 6743 Z= 0.276 Chirality : 0.043 0.215 754 Planarity : 0.004 0.046 871 Dihedral : 3.897 19.420 692 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.47 (0.32), residues: 620 helix: -3.50 (0.67), residues: 34 sheet: 0.25 (0.40), residues: 172 loop : -1.36 (0.28), residues: 414 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 0.623 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 75 average time/residue: 0.1935 time to fit residues: 18.3254 Evaluate side-chains 70 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 0.507 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0467 time to fit residues: 0.7749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 6.9990 chunk 48 optimal weight: 0.0070 chunk 5 optimal weight: 0.8980 chunk 37 optimal weight: 10.0000 chunk 29 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 185 HIS H 218 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 4950 Z= 0.175 Angle : 0.549 7.610 6743 Z= 0.272 Chirality : 0.043 0.211 754 Planarity : 0.004 0.047 871 Dihedral : 3.830 19.911 692 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.44 (0.32), residues: 620 helix: -3.45 (0.68), residues: 34 sheet: 0.25 (0.40), residues: 172 loop : -1.34 (0.28), residues: 414 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 73 time to evaluate : 0.620 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 75 average time/residue: 0.2265 time to fit residues: 21.4779 Evaluate side-chains 71 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 0.564 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0571 time to fit residues: 0.9158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 0.0270 chunk 2 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 32 optimal weight: 0.5980 chunk 41 optimal weight: 0.0010 overall best weight: 0.4644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 185 HIS H 218 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.188144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.181076 restraints weight = 6294.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.180691 restraints weight = 16406.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.180659 restraints weight = 15506.205| |-----------------------------------------------------------------------------| r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 4950 Z= 0.156 Angle : 0.541 7.425 6743 Z= 0.268 Chirality : 0.043 0.215 754 Planarity : 0.004 0.047 871 Dihedral : 3.758 18.985 692 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.34 (0.32), residues: 620 helix: -3.42 (0.69), residues: 34 sheet: 0.39 (0.41), residues: 168 loop : -1.28 (0.29), residues: 418 =============================================================================== Job complete usr+sys time: 1304.48 seconds wall clock time: 24 minutes 33.00 seconds (1473.00 seconds total)