Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:47:55 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ji0_22341/11_2022/7ji0_22341.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ji0_22341/11_2022/7ji0_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_22341/11_2022/7ji0_22341.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ji0_22341/11_2022/7ji0_22341.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ji0_22341/11_2022/7ji0_22341.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ji0_22341/11_2022/7ji0_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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" 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-4778/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: 2.51, 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: 1.46 Conformation dependent library (CDL) restraints added in 526.5 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: 0.82 Time building geometry restraints manager: 1.58 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: 0.770 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: 3.800 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.030 Process input model: 14.680 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.500 ------------------------------------------------------------------------------- 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 : 4.08 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 : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 5 residues processed: 74 average time/residue: 1.0528 time to fit residues: 80.6779 Evaluate side-chains 48 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.409 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 0.6029 ------------------------------------------------------------------------------- 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: 0.8980 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.0050 chunk 36 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.8996 ------------------------------------------------------------------------------- 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 186 ASN A 209 ASN A 230 GLN B 175 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 3616 Z= 0.223 Angle : 0.493 3.865 4888 Z= 0.268 Chirality : 0.038 0.130 568 Planarity : 0.003 0.028 610 Dihedral : 4.282 16.314 462 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % 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: -1.12 (0.39), residues: 420 helix: -0.11 (0.28), residues: 328 sheet: None (None), residues: 0 loop : -2.76 (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 54 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 41 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 54 average time/residue: 0.9837 time to fit residues: 55.1202 Evaluate side-chains 41 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 0.312 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.4322 ------------------------------------------------------------------------------- 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: 0.5980 chunk 24 optimal weight: 0.9980 chunk 10 optimal weight: 0.2980 chunk 36 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 209 ASN B 223 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.059 3616 Z= 0.154 Angle : 0.437 6.078 4888 Z= 0.236 Chirality : 0.037 0.123 568 Planarity : 0.002 0.030 610 Dihedral : 4.008 15.966 462 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.94 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: -0.15 (0.40), residues: 420 helix: 0.58 (0.29), residues: 330 sheet: None (None), residues: 0 loop : -2.47 (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 54 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 41 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 54 average time/residue: 1.0607 time to fit residues: 59.4333 Evaluate side-chains 40 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 time to evaluate : 0.425 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 0.5990 ------------------------------------------------------------------------------- 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: 1.9990 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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: 0.8366 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.030 3616 Z= 0.292 Angle : 0.535 7.860 4888 Z= 0.279 Chirality : 0.041 0.199 568 Planarity : 0.003 0.030 610 Dihedral : 4.254 16.509 462 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer Outliers : 4.19 % 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: -0.03 (0.40), residues: 420 helix: 0.63 (0.28), residues: 330 sheet: None (None), residues: 0 loop : -2.29 (0.60), residues: 90 *********************** 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 57 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 40 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 55 average time/residue: 1.0174 time to fit residues: 58.0963 Evaluate side-chains 46 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 37 time to evaluate : 0.487 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 1.3129 time to fit residues: 1.9080 ------------------------------------------------------------------------------- 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: 0.7980 chunk 26 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 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: 0.8310 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 3616 Z= 0.169 Angle : 0.460 6.419 4888 Z= 0.247 Chirality : 0.038 0.188 568 Planarity : 0.002 0.030 610 Dihedral : 3.968 15.705 462 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer Outliers : 2.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.41), residues: 420 helix: 0.87 (0.29), residues: 334 sheet: None (None), residues: 0 loop : -1.92 (0.61), residues: 86 *********************** 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: 11 poor density : 39 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 50 average time/residue: 1.0645 time to fit residues: 55.2878 Evaluate side-chains 40 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 32 time to evaluate : 0.441 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 0.6113 ------------------------------------------------------------------------------- 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: 0.5980 chunk 38 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.8334 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 3616 Z= 0.201 Angle : 0.477 6.504 4888 Z= 0.250 Chirality : 0.039 0.168 568 Planarity : 0.002 0.030 610 Dihedral : 3.978 15.713 462 Min Nonbonded Distance : 2.241 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: 0.56 (0.41), residues: 420 helix: 0.97 (0.29), residues: 334 sheet: None (None), residues: 0 loop : -1.87 (0.61), residues: 86 *********************** 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 52 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 39 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 51 average time/residue: 1.1952 time to fit residues: 63.1211 Evaluate side-chains 43 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 35 time to evaluate : 0.434 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 0.6028 ------------------------------------------------------------------------------- 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: 0.3980 chunk 32 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8325 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.075 3616 Z= 0.195 Angle : 0.467 5.206 4888 Z= 0.250 Chirality : 0.038 0.155 568 Planarity : 0.002 0.030 610 Dihedral : 3.903 15.349 462 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % 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: 0.81 (0.41), residues: 420 helix: 1.19 (0.29), residues: 330 sheet: None (None), residues: 0 loop : -1.84 (0.59), 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 47 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 37 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 46 average time/residue: 1.1632 time to fit residues: 55.4549 Evaluate side-chains 44 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 36 time to evaluate : 0.404 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 0.5612 ------------------------------------------------------------------------------- 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: 0.3980 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 23 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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: 0.8309 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.050 3616 Z= 0.155 Angle : 0.437 5.111 4888 Z= 0.235 Chirality : 0.037 0.147 568 Planarity : 0.002 0.030 610 Dihedral : 3.798 14.860 462 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % 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: 1.04 (0.41), residues: 420 helix: 1.38 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -1.78 (0.58), residues: 92 *********************** 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 45 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 35 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 45 average time/residue: 1.0925 time to fit residues: 51.1141 Evaluate side-chains 41 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 33 time to evaluate : 0.410 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 0.5901 ------------------------------------------------------------------------------- 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: 0.0870 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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: 0.8318 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 3616 Z= 0.175 Angle : 0.451 5.251 4888 Z= 0.241 Chirality : 0.038 0.141 568 Planarity : 0.002 0.030 610 Dihedral : 3.822 14.874 462 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.22 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: 1.10 (0.41), residues: 420 helix: 1.39 (0.29), residues: 330 sheet: None (None), residues: 0 loop : -1.68 (0.58), 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 44 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 34 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 44 average time/residue: 1.1250 time to fit residues: 51.4153 Evaluate side-chains 41 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 33 time to evaluate : 0.435 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 0.5992 ------------------------------------------------------------------------------- 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: 0.9990 chunk 9 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 32 optimal weight: 0.6980 chunk 5 optimal weight: 0.3980 chunk 27 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.8311 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 3616 Z= 0.169 Angle : 0.449 5.383 4888 Z= 0.241 Chirality : 0.038 0.139 568 Planarity : 0.002 0.030 610 Dihedral : 3.785 14.561 462 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer Outliers : 2.22 % 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: 1.20 (0.41), residues: 420 helix: 1.48 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -1.68 (0.57), 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: 9 poor density : 37 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 46 average time/residue: 1.1772 time to fit residues: 56.1871 Evaluate side-chains 40 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 32 time to evaluate : 0.433 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 0.6082 ------------------------------------------------------------------------------- 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: 0.0670 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 0.0270 chunk 1 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.124319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.107239 restraints weight = 4271.116| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.01 r_work: 0.3296 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 1.81 restraints_weight: 0.2500 r_work: 0.3272 rms_B_bonded: 1.85 restraints_weight: 0.1250 r_work: 0.3259 rms_B_bonded: 1.93 restraints_weight: 0.0625 r_work: 0.3246 rms_B_bonded: 2.04 restraints_weight: 0.0312 r_work: 0.3232 rms_B_bonded: 2.18 restraints_weight: 0.0156 r_work: 0.3217 rms_B_bonded: 2.35 restraints_weight: 0.0078 r_work: 0.3201 rms_B_bonded: 2.55 restraints_weight: 0.0039 r_work: 0.3184 rms_B_bonded: 2.78 restraints_weight: 0.0020 r_work: 0.3166 rms_B_bonded: 3.05 restraints_weight: 0.0010 r_work: 0.3146 rms_B_bonded: 3.35 restraints_weight: 0.0005 r_work: 0.3125 rms_B_bonded: 3.68 restraints_weight: 0.0002 r_work: 0.3102 rms_B_bonded: 4.06 restraints_weight: 0.0001 r_work: 0.3078 rms_B_bonded: 4.48 restraints_weight: 0.0001 r_work: 0.3051 rms_B_bonded: 4.95 restraints_weight: 0.0000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.075 3616 Z= 0.155 Angle : 0.435 5.066 4888 Z= 0.236 Chirality : 0.037 0.136 568 Planarity : 0.002 0.030 610 Dihedral : 3.683 14.037 462 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer Outliers : 2.22 % 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: 1.32 (0.41), residues: 420 helix: 1.56 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -1.61 (0.58), residues: 92 =============================================================================== Job complete usr+sys time: 1525.03 seconds wall clock time: 28 minutes 12.43 seconds (1692.43 seconds total)