Starting phenix.real_space_refine (version: dev) on Fri Feb 17 05:57:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ji0_22341/02_2023/7ji0_22341.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ji0_22341/02_2023/7ji0_22341.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ji0_22341/02_2023/7ji0_22341.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ji0_22341/02_2023/7ji0_22341.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ji0_22341/02_2023/7ji0_22341.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ji0_22341/02_2023/7ji0_22341.pdb" } resolution = 2.95 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= 0.099 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 84": "NH1" <-> "NH2" Residue "A ARG 159": "NH1" <-> "NH2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 216": "OE1" <-> "OE2" Residue "B ARG 244": "NH1" <-> "NH2" Residue "B PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 3556 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1722 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 2, 'TRANS': 205} Chain breaks: 1 Chain: "B" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1722 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 2, 'TRANS': 205} Chain breaks: 1 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 56 Classifications: {'peptide': 8} Modifications used: {'COO': 1} Link IDs: {'TRANS': 7} Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 56 Classifications: {'peptide': 8} Modifications used: {'COO': 1} Link IDs: {'TRANS': 7} Time building chain proxies: 2.54, per 1000 atoms: 0.71 Number of scatterers: 3556 At special positions: 0 Unit cell: (78.888, 73.698, 63.318, 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 16 16.00 O 684 8.00 N 558 7.00 C 2298 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: 1.51 Conformation dependent library (CDL) restraints added in 489.2 milliseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 836 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 0 sheets defined 73.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 74 through 89 removed outlier: 3.854A pdb=" N ASN A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 123 removed outlier: 3.701A pdb=" N THR A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET A 114 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR A 121 " --> pdb=" O SER A 117 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N MET A 122 " --> pdb=" O ILE A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 141 Processing helix chain 'A' and resid 147 through 156 removed outlier: 3.511A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE A 152 " --> pdb=" O TYR A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 174 removed outlier: 3.698A pdb=" N LEU A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 169 " --> pdb=" O SER A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 204 removed outlier: 3.950A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A 193 " --> pdb=" O ILE A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 221 removed outlier: 3.513A pdb=" N PHE A 211 " --> pdb=" O PHE A 207 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TYR A 212 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A 219 " --> pdb=" O ASP A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 245 removed outlier: 3.518A pdb=" N TRP A 245 " --> pdb=" O GLU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 264 Processing helix chain 'A' and resid 266 through 282 removed outlier: 3.873A pdb=" N LEU A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N HIS A 272 " --> pdb=" O ASN A 268 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS A 276 " --> pdb=" O HIS A 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 89 removed outlier: 3.754A pdb=" N ASN B 78 " --> pdb=" O GLU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 96 removed outlier: 3.757A pdb=" N ILE B 95 " --> pdb=" O ASN B 91 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN B 96 " --> pdb=" O ILE B 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 91 through 96' Processing helix chain 'B' and resid 108 through 120 Processing helix chain 'B' and resid 129 through 142 removed outlier: 3.677A pdb=" N TYR B 139 " --> pdb=" O GLN B 135 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS B 142 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 156 removed outlier: 3.787A pdb=" N ILE B 152 " --> pdb=" O TYR B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.717A pdb=" N LEU B 168 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 169 " --> pdb=" O SER B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 204 removed outlier: 3.983A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE B 189 " --> pdb=" O THR B 185 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL B 190 " --> pdb=" O ASN B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 221 removed outlier: 3.631A pdb=" N PHE B 211 " --> pdb=" O PHE B 207 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N TYR B 212 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU B 213 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA B 219 " --> pdb=" O ASP B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 245 Processing helix chain 'B' and resid 247 through 264 removed outlier: 4.151A pdb=" N ILE B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU B 252 " --> pdb=" O THR B 248 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS B 253 " --> pdb=" O SER B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 282 removed outlier: 3.503A pdb=" N LYS B 279 " --> pdb=" O ILE B 275 " (cutoff:3.500A) 193 hydrogen bonds defined for protein. 579 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: 0.84 Time building geometry restraints manager: 1.59 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: 1120 1.34 - 1.46: 699 1.46 - 1.57: 1771 1.57 - 1.69: 0 1.69 - 1.81: 26 Bond restraints: 3616 Sorted by residual: bond pdb=" CB ILE B 189 " pdb=" CG2 ILE B 189 " ideal model delta sigma weight residual 1.521 1.502 0.019 3.30e-02 9.18e+02 3.40e-01 bond pdb=" CG PRO A 109 " pdb=" CD PRO A 109 " ideal model delta sigma weight residual 1.503 1.486 0.017 3.40e-02 8.65e+02 2.45e-01 bond pdb=" CA LEU A 269 " pdb=" CB LEU A 269 " ideal model delta sigma weight residual 1.537 1.528 0.008 1.67e-02 3.59e+03 2.44e-01 bond pdb=" CZ ARG A 159 " pdb=" NH2 ARG A 159 " ideal model delta sigma weight residual 1.330 1.324 0.006 1.30e-02 5.92e+03 2.40e-01 bond pdb=" CZ ARG B 159 " pdb=" NH2 ARG B 159 " ideal model delta sigma weight residual 1.330 1.324 0.006 1.30e-02 5.92e+03 2.34e-01 ... (remaining 3611 not shown) Histogram of bond angle deviations from ideal: 100.50 - 107.19: 48 107.19 - 113.88: 2082 113.88 - 120.57: 1541 120.57 - 127.26: 1200 127.26 - 133.95: 17 Bond angle restraints: 4888 Sorted by residual: angle pdb=" N LEU A 269 " pdb=" CA LEU A 269 " pdb=" C LEU A 269 " ideal model delta sigma weight residual 114.04 109.16 4.88 1.24e+00 6.50e-01 1.55e+01 angle pdb=" C ILE A 92 " pdb=" N ASN A 93 " pdb=" CA ASN A 93 " ideal model delta sigma weight residual 121.54 126.27 -4.73 1.91e+00 2.74e-01 6.14e+00 angle pdb=" C ASN B 104 " pdb=" N TYR B 105 " pdb=" CA TYR B 105 " ideal model delta sigma weight residual 121.54 125.17 -3.63 1.91e+00 2.74e-01 3.61e+00 angle pdb=" CA LEU A 269 " pdb=" C LEU A 269 " pdb=" N LYS A 270 " ideal model delta sigma weight residual 118.58 116.45 2.13 1.26e+00 6.30e-01 2.86e+00 angle pdb=" C GLY B 155 " pdb=" N ASN B 156 " pdb=" CA ASN B 156 " ideal model delta sigma weight residual 122.27 119.22 3.05 1.85e+00 2.92e-01 2.71e+00 ... (remaining 4883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 2004 17.23 - 34.45: 121 34.45 - 51.68: 34 51.68 - 68.90: 3 68.90 - 86.13: 6 Dihedral angle restraints: 2168 sinusoidal: 880 harmonic: 1288 Sorted by residual: dihedral pdb=" CA ASN A 94 " pdb=" C ASN A 94 " pdb=" N ILE A 95 " pdb=" CA ILE A 95 " ideal model delta harmonic sigma weight residual 180.00 163.46 16.54 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CB GLU B 74 " pdb=" CG GLU B 74 " pdb=" CD GLU B 74 " pdb=" OE1 GLU B 74 " ideal model delta sinusoidal sigma weight residual 0.00 86.13 -86.13 1 3.00e+01 1.11e-03 9.95e+00 dihedral pdb=" CB GLU A 74 " pdb=" CG GLU A 74 " pdb=" CD GLU A 74 " pdb=" OE1 GLU A 74 " ideal model delta sinusoidal sigma weight residual 0.00 84.80 -84.80 1 3.00e+01 1.11e-03 9.70e+00 ... (remaining 2165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 292 0.026 - 0.053: 179 0.053 - 0.079: 77 0.079 - 0.105: 15 0.105 - 0.132: 5 Chirality restraints: 568 Sorted by residual: chirality pdb=" CA PRO B 109 " pdb=" N PRO B 109 " pdb=" C PRO B 109 " pdb=" CB PRO B 109 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CA PRO A 109 " pdb=" N PRO A 109 " pdb=" C PRO A 109 " pdb=" CB PRO A 109 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CA ILE A 92 " pdb=" N ILE A 92 " pdb=" C ILE A 92 " pdb=" CB ILE A 92 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 565 not shown) Planarity restraints: 610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 127 " 0.019 5.00e-02 4.00e+02 2.89e-02 1.34e+00 pdb=" N PRO A 128 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 128 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 128 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 273 " 0.005 2.00e-02 2.50e+03 1.03e-02 1.05e+00 pdb=" C TYR B 273 " -0.018 2.00e-02 2.50e+03 pdb=" O TYR B 273 " 0.007 2.00e-02 2.50e+03 pdb=" N THR B 274 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 232 " 0.005 2.00e-02 2.50e+03 1.01e-02 1.02e+00 pdb=" C VAL A 232 " -0.017 2.00e-02 2.50e+03 pdb=" O VAL A 232 " 0.006 2.00e-02 2.50e+03 pdb=" N PHE A 233 " 0.006 2.00e-02 2.50e+03 ... (remaining 607 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 651 2.77 - 3.30: 3491 3.30 - 3.83: 5341 3.83 - 4.37: 6765 4.37 - 4.90: 11609 Nonbonded interactions: 27857 Sorted by model distance: nonbonded pdb=" O LYS B 279 " pdb=" ND2 ASN B 283 " model vdw 2.233 2.520 nonbonded pdb=" O LYS A 279 " pdb=" ND2 ASN A 283 " model vdw 2.249 2.520 nonbonded pdb=" OD2 ASP B 123 " pdb=" OG SER B 125 " model vdw 2.287 2.440 nonbonded pdb=" OH TYR A 82 " pdb=" ND2 ASN A 94 " model vdw 2.303 2.520 nonbonded pdb=" O ASP B 278 " pdb=" ND2 ASN B 282 " model vdw 2.335 2.520 ... (remaining 27852 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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 16 5.16 5 C 2298 2.51 5 N 558 2.21 5 O 684 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.160 Check model and map are aligned: 0.050 Process input model: 14.060 Find NCS groups from input model: 0.180 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: 0.000 Load rotamer database and sin/cos tables:14.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 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 0.019 3616 Z= 0.213 Angle : 0.475 4.879 4888 Z= 0.281 Chirality : 0.038 0.132 568 Planarity : 0.003 0.029 610 Dihedral : 12.973 86.129 1332 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer Outliers : 5.91 % 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: -3.04 (0.33), residues: 420 helix: -1.46 (0.24), residues: 330 sheet: None (None), residues: 0 loop : -3.52 (0.47), residues: 90 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 54 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 5 residues processed: 74 average time/residue: 1.1663 time to fit residues: 89.1393 Evaluate side-chains 48 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.467 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 0.6054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 31 optimal weight: 0.3980 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.0050 chunk 36 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 GLN A 230 GLN B 175 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 3616 Z= 0.195 Angle : 0.475 3.816 4888 Z= 0.259 Chirality : 0.038 0.126 568 Planarity : 0.003 0.028 610 Dihedral : 4.208 16.173 462 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer Outliers : 2.96 % 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: -1.07 (0.39), residues: 420 helix: -0.08 (0.28), residues: 328 sheet: None (None), residues: 0 loop : -2.75 (0.53), residues: 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 44 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 56 average time/residue: 1.1011 time to fit residues: 63.8609 Evaluate side-chains 41 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.399 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 0.5470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 0.2980 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 0.0670 chunk 18 optimal weight: 0.8980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 ASN B 209 ASN B 223 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.057 3616 Z= 0.153 Angle : 0.431 5.807 4888 Z= 0.232 Chirality : 0.036 0.123 568 Planarity : 0.002 0.030 610 Dihedral : 3.963 15.806 462 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer Outliers : 3.20 % 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: -0.14 (0.40), residues: 420 helix: 0.58 (0.29), residues: 330 sheet: None (None), residues: 0 loop : -2.44 (0.56), residues: 90 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 40 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 53 average time/residue: 1.2345 time to fit residues: 67.7778 Evaluate side-chains 40 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 time to evaluate : 0.434 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 0.6088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 3616 Z= 0.190 Angle : 0.477 7.523 4888 Z= 0.251 Chirality : 0.039 0.207 568 Planarity : 0.002 0.030 610 Dihedral : 3.974 15.569 462 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer Outliers : 3.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.41), residues: 420 helix: 0.73 (0.28), residues: 334 sheet: None (None), residues: 0 loop : -2.05 (0.60), residues: 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 36 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 51 average time/residue: 1.2751 time to fit residues: 67.1681 Evaluate side-chains 42 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 34 time to evaluate : 0.385 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 0.5308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 0.0040 chunk 22 optimal weight: 0.0870 overall best weight: 0.3770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 3616 Z= 0.118 Angle : 0.425 6.158 4888 Z= 0.227 Chirality : 0.037 0.183 568 Planarity : 0.002 0.031 610 Dihedral : 3.739 14.366 462 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer Outliers : 2.96 % 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: 0.68 (0.41), residues: 420 helix: 1.13 (0.29), residues: 330 sheet: None (None), residues: 0 loop : -2.03 (0.58), residues: 90 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 38 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 49 average time/residue: 1.1809 time to fit residues: 60.0130 Evaluate side-chains 46 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 37 time to evaluate : 0.414 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 0 time to fit residues: 0.5608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 3616 Z= 0.207 Angle : 0.467 5.683 4888 Z= 0.246 Chirality : 0.039 0.167 568 Planarity : 0.002 0.030 610 Dihedral : 3.894 14.679 462 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer Outliers : 3.45 % 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: 0.79 (0.41), residues: 420 helix: 1.17 (0.29), residues: 330 sheet: None (None), residues: 0 loop : -1.83 (0.61), residues: 90 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 39 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 51 average time/residue: 1.2503 time to fit residues: 65.9827 Evaluate side-chains 44 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 35 time to evaluate : 0.432 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 1.6763 time to fit residues: 2.3233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 3616 Z= 0.195 Angle : 0.469 5.088 4888 Z= 0.248 Chirality : 0.039 0.154 568 Planarity : 0.002 0.031 610 Dihedral : 3.909 15.071 462 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer Outliers : 2.96 % 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: 0.86 (0.41), residues: 420 helix: 1.23 (0.29), residues: 330 sheet: None (None), residues: 0 loop : -1.85 (0.60), residues: 90 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 37 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 48 average time/residue: 1.2124 time to fit residues: 60.2251 Evaluate side-chains 45 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 0.410 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 0.6288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.1980 chunk 30 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.093 3616 Z= 0.179 Angle : 0.442 5.126 4888 Z= 0.240 Chirality : 0.037 0.142 568 Planarity : 0.002 0.030 610 Dihedral : 3.791 14.511 462 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer Outliers : 3.20 % 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: 1.03 (0.41), residues: 420 helix: 1.36 (0.29), residues: 330 sheet: None (None), residues: 0 loop : -1.84 (0.59), residues: 90 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 39 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 49 average time/residue: 1.3066 time to fit residues: 66.2976 Evaluate side-chains 45 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 36 time to evaluate : 0.459 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 1.7346 time to fit residues: 2.3616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.7980 chunk 23 optimal weight: 0.0470 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 0.0970 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.099 3616 Z= 0.172 Angle : 0.443 5.307 4888 Z= 0.241 Chirality : 0.037 0.139 568 Planarity : 0.002 0.031 610 Dihedral : 3.701 14.130 462 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer Outliers : 2.46 % 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: 1.19 (0.41), residues: 420 helix: 1.46 (0.29), residues: 330 sheet: None (None), residues: 0 loop : -1.69 (0.59), residues: 90 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 39 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 49 average time/residue: 1.3273 time to fit residues: 67.3104 Evaluate side-chains 43 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 35 time to evaluate : 0.421 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 0.5793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 5 optimal weight: 0.0980 chunk 27 optimal weight: 0.3980 chunk 1 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 3616 Z= 0.161 Angle : 0.473 11.761 4888 Z= 0.244 Chirality : 0.038 0.141 568 Planarity : 0.002 0.030 610 Dihedral : 3.848 20.229 462 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer Outliers : 1.97 % 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: 1.31 (0.41), residues: 420 helix: 1.56 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -1.65 (0.59), residues: 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 38 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 8 residues processed: 46 average time/residue: 1.0753 time to fit residues: 51.5334 Evaluate side-chains 45 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 0.452 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 0.6292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.0870 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 0.0670 chunk 1 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.4980 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 39 optimal weight: 0.3980 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.126751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.109599 restraints weight = 4269.648| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.00 r_work: 0.3219 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.062 3616 Z= 0.131 Angle : 0.412 5.443 4888 Z= 0.224 Chirality : 0.036 0.132 568 Planarity : 0.002 0.031 610 Dihedral : 3.625 15.076 462 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer Outliers : 2.46 % 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: 1.48 (0.42), residues: 420 helix: 1.68 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -1.60 (0.58), residues: 92 =============================================================================== Job complete usr+sys time: 1698.29 seconds wall clock time: 30 minutes 56.52 seconds (1856.52 seconds total)