Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 14:25:14 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlv_11275/12_2021/6zlv_11275.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlv_11275/12_2021/6zlv_11275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlv_11275/12_2021/6zlv_11275.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlv_11275/12_2021/6zlv_11275.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlv_11275/12_2021/6zlv_11275.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlv_11275/12_2021/6zlv_11275.pdb" } resolution = 3.5 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model 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 None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/chem_data/mon_lib" Total number of atoms: 5352 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1338 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 10, 'TRANS': 165} Chain: "B" Number of atoms: 1338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1338 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 10, 'TRANS': 165} Chain: "C" Number of atoms: 1338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1338 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 10, 'TRANS': 165} Chain: "D" Number of atoms: 1338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1338 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 10, 'TRANS': 165} Time building chain proxies: 3.30, per 1000 atoms: 0.62 Number of scatterers: 5352 At special positions: 0 Unit cell: (75.978, 79.596, 121.806, 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 1012 8.00 N 944 7.00 C 3380 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 Amimo 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: 2.12 Conformation dependent library (CDL) restraints added in 812.3 milliseconds 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1296 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 8 sheets defined 14.3% alpha, 39.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 79 through 94 removed outlier: 3.586A pdb=" N GLU A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 128 Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'B' and resid 80 through 94 Processing helix chain 'B' and resid 124 through 128 Processing helix chain 'B' and resid 243 through 247 Processing helix chain 'C' and resid 80 through 94 Processing helix chain 'C' and resid 124 through 128 Processing helix chain 'C' and resid 243 through 247 Processing helix chain 'D' and resid 80 through 94 Processing helix chain 'D' and resid 124 through 128 Processing helix chain 'D' and resid 243 through 247 Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 110 removed outlier: 4.218A pdb=" N GLY A 109 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N LEU A 156 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VAL A 145 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL A 135 " --> pdb=" O MET A 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 164 through 169 removed outlier: 4.222A pdb=" N VAL A 236 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N VAL A 239 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N VAL A 222 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N SER A 206 " --> pdb=" O PRO A 218 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 110 removed outlier: 4.248A pdb=" N GLY B 109 " --> pdb=" O MET B 120 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N LEU B 156 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N VAL B 145 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL B 135 " --> pdb=" O MET B 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 164 through 169 removed outlier: 4.209A pdb=" N VAL B 236 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N VAL B 239 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N VAL B 222 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N SER B 206 " --> pdb=" O PRO B 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 102 through 110 removed outlier: 4.238A pdb=" N GLY C 109 " --> pdb=" O MET C 120 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LEU C 156 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N VAL C 145 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL C 135 " --> pdb=" O MET C 142 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 164 through 169 removed outlier: 4.241A pdb=" N VAL C 236 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N VAL C 239 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N VAL C 222 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N SER C 206 " --> pdb=" O PRO C 218 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 102 through 110 removed outlier: 4.209A pdb=" N GLY D 109 " --> pdb=" O MET D 120 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LEU D 156 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N VAL D 145 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL D 135 " --> pdb=" O MET D 142 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 164 through 169 removed outlier: 4.244A pdb=" N VAL D 236 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N VAL D 239 " --> pdb=" O VAL D 222 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N VAL D 222 " --> pdb=" O VAL D 239 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N SER D 206 " --> pdb=" O PRO D 218 " (cutoff:3.500A) 196 hydrogen bonds defined for protein. 504 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.41 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1121 1.33 - 1.45: 1188 1.45 - 1.57: 3088 1.57 - 1.70: 3 1.70 - 1.82: 32 Bond restraints: 5432 Sorted by residual: bond pdb=" C ILE B 108 " pdb=" N GLY B 109 " ideal model delta sigma weight residual 1.332 1.354 -0.022 6.60e-03 2.30e+04 1.16e+01 bond pdb=" C ILE C 108 " pdb=" N GLY C 109 " ideal model delta sigma weight residual 1.332 1.354 -0.022 6.60e-03 2.30e+04 1.08e+01 bond pdb=" C ILE D 108 " pdb=" N GLY D 109 " ideal model delta sigma weight residual 1.332 1.352 -0.020 6.60e-03 2.30e+04 9.55e+00 bond pdb=" C ILE A 108 " pdb=" N GLY A 109 " ideal model delta sigma weight residual 1.332 1.352 -0.020 6.60e-03 2.30e+04 9.09e+00 bond pdb=" C VAL A 236 " pdb=" O VAL A 236 " ideal model delta sigma weight residual 1.237 1.205 0.032 1.09e-02 8.42e+03 8.70e+00 ... (remaining 5427 not shown) Histogram of bond angle deviations from ideal: 95.81 - 102.96: 52 102.96 - 110.11: 1199 110.11 - 117.26: 2913 117.26 - 124.41: 2944 124.41 - 131.55: 288 Bond angle restraints: 7396 Sorted by residual: angle pdb=" C THR A 82 " pdb=" N GLU A 83 " pdb=" CA GLU A 83 " ideal model delta sigma weight residual 120.54 128.15 -7.61 1.35e+00 5.49e-01 3.18e+01 angle pdb=" C THR C 82 " pdb=" N GLU C 83 " pdb=" CA GLU C 83 " ideal model delta sigma weight residual 120.54 128.11 -7.57 1.35e+00 5.49e-01 3.14e+01 angle pdb=" C THR D 82 " pdb=" N GLU D 83 " pdb=" CA GLU D 83 " ideal model delta sigma weight residual 120.54 128.06 -7.52 1.35e+00 5.49e-01 3.10e+01 angle pdb=" C THR B 82 " pdb=" N GLU B 83 " pdb=" CA GLU B 83 " ideal model delta sigma weight residual 120.54 127.97 -7.43 1.35e+00 5.49e-01 3.03e+01 angle pdb=" CB ARG D 175 " pdb=" CG ARG D 175 " pdb=" CD ARG D 175 " ideal model delta sigma weight residual 111.30 122.99 -11.69 2.30e+00 1.89e-01 2.58e+01 ... (remaining 7391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.79: 3103 15.79 - 31.57: 139 31.57 - 47.35: 60 47.35 - 63.14: 14 63.14 - 78.92: 4 Dihedral angle restraints: 3320 sinusoidal: 1308 harmonic: 2012 Sorted by residual: dihedral pdb=" C THR C 241 " pdb=" N THR C 241 " pdb=" CA THR C 241 " pdb=" CB THR C 241 " ideal model delta harmonic sigma weight residual -122.00 -132.49 10.49 0 2.50e+00 1.60e-01 1.76e+01 dihedral pdb=" C THR A 241 " pdb=" N THR A 241 " pdb=" CA THR A 241 " pdb=" CB THR A 241 " ideal model delta harmonic sigma weight residual -122.00 -132.16 10.16 0 2.50e+00 1.60e-01 1.65e+01 dihedral pdb=" C THR B 241 " pdb=" N THR B 241 " pdb=" CA THR B 241 " pdb=" CB THR B 241 " ideal model delta harmonic sigma weight residual -122.00 -131.88 9.88 0 2.50e+00 1.60e-01 1.56e+01 ... (remaining 3317 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 451 0.079 - 0.158: 276 0.158 - 0.237: 128 0.237 - 0.316: 27 0.316 - 0.395: 14 Chirality restraints: 896 Sorted by residual: chirality pdb=" CA SER D 139 " pdb=" N SER D 139 " pdb=" C SER D 139 " pdb=" CB SER D 139 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" CG LEU B 204 " pdb=" CB LEU B 204 " pdb=" CD1 LEU B 204 " pdb=" CD2 LEU B 204 " both_signs ideal model delta sigma weight residual False -2.59 -2.20 -0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" CA SER A 139 " pdb=" N SER A 139 " pdb=" C SER A 139 " pdb=" CB SER A 139 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.64e+00 ... (remaining 893 not shown) Planarity restraints: 972 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE D 108 " -0.022 2.00e-02 2.50e+03 4.36e-02 1.90e+01 pdb=" C ILE D 108 " 0.075 2.00e-02 2.50e+03 pdb=" O ILE D 108 " -0.028 2.00e-02 2.50e+03 pdb=" N GLY D 109 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 108 " -0.021 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" C ILE B 108 " 0.072 2.00e-02 2.50e+03 pdb=" O ILE B 108 " -0.027 2.00e-02 2.50e+03 pdb=" N GLY B 109 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 108 " -0.020 2.00e-02 2.50e+03 4.07e-02 1.66e+01 pdb=" C ILE C 108 " 0.070 2.00e-02 2.50e+03 pdb=" O ILE C 108 " -0.026 2.00e-02 2.50e+03 pdb=" N GLY C 109 " -0.024 2.00e-02 2.50e+03 ... (remaining 969 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 663 2.76 - 3.29: 5020 3.29 - 3.83: 8521 3.83 - 4.36: 10848 4.36 - 4.90: 18243 Nonbonded interactions: 43295 Sorted by model distance: nonbonded pdb=" OE1 GLU C 188 " pdb=" NH2 ARG D 190 " model vdw 2.221 2.520 nonbonded pdb=" NH2 ARG C 190 " pdb=" OE1 GLU D 188 " model vdw 2.230 2.520 nonbonded pdb=" OE1 GLN D 117 " pdb=" OG1 THR D 159 " model vdw 2.238 2.440 nonbonded pdb=" OE1 GLU A 188 " pdb=" NH2 ARG B 190 " model vdw 2.239 2.520 nonbonded pdb=" OE1 GLN B 117 " pdb=" OG1 THR B 159 " model vdw 2.240 2.440 ... (remaining 43290 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' selection = 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 3380 2.51 5 N 944 2.21 5 O 1012 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Write .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 8.660 Check model and map are aligned: 0.080 Convert atoms to be neutral: 0.050 Process input model: 17.840 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 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:2.250 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 30.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 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 : 0.011 0.058 5432 Z= 0.689 Angle : 1.856 11.693 7396 Z= 1.212 Chirality : 0.120 0.395 896 Planarity : 0.010 0.049 972 Dihedral : 12.218 78.921 2024 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.57 % Allowed : 3.74 % Favored : 95.69 % Rotamer Outliers : 2.72 % Cbeta Deviations : 0.62 % 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: -1.53 (0.30), residues: 696 helix: -3.69 (0.38), residues: 64 sheet: -0.88 (0.30), residues: 256 loop : -0.47 (0.32), residues: 376 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 163 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 0 residues processed: 174 average time/residue: 0.2109 time to fit residues: 44.7333 Evaluate side-chains 89 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.631 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 17 optimal weight: 20.0000 chunk 34 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 53 optimal weight: 0.3980 chunk 20 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 overall best weight: 5.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 144 GLN A 168 GLN B 133 GLN B 144 GLN B 168 GLN C 113 ASN ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 ASN C 144 GLN C 168 GLN ** D 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 144 GLN D 168 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.042 5432 Z= 0.394 Angle : 0.810 6.938 7396 Z= 0.409 Chirality : 0.053 0.153 896 Planarity : 0.007 0.099 972 Dihedral : 5.218 18.307 764 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 3.06 % 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: -0.21 (0.32), residues: 696 helix: 1.27 (0.59), residues: 64 sheet: -0.48 (0.31), residues: 300 loop : 0.10 (0.33), residues: 332 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 95 time to evaluate : 0.728 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 109 average time/residue: 0.2013 time to fit residues: 27.4812 Evaluate side-chains 84 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 0.570 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0475 time to fit residues: 1.4611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 42 optimal weight: 8.9990 chunk 17 optimal weight: 20.0000 chunk 61 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 GLN ** D 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 5432 Z= 0.244 Angle : 0.687 6.763 7396 Z= 0.338 Chirality : 0.049 0.148 896 Planarity : 0.005 0.064 972 Dihedral : 4.649 15.401 764 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer Outliers : 1.02 % 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: 0.29 (0.33), residues: 696 helix: 3.08 (0.61), residues: 64 sheet: -0.51 (0.31), residues: 288 loop : 0.47 (0.34), residues: 344 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 83 time to evaluate : 0.634 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 86 average time/residue: 0.1886 time to fit residues: 20.7642 Evaluate side-chains 74 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 0.683 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0491 time to fit residues: 1.3326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 32 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 58 optimal weight: 0.0060 chunk 17 optimal weight: 20.0000 chunk 54 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 overall best weight: 3.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN C 84 GLN ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.5625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 5432 Z= 0.243 Angle : 0.666 7.181 7396 Z= 0.325 Chirality : 0.049 0.132 896 Planarity : 0.005 0.052 972 Dihedral : 4.505 14.904 764 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 1.19 % 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: 0.25 (0.33), residues: 696 helix: 3.50 (0.62), residues: 64 sheet: -0.77 (0.30), residues: 288 loop : 0.59 (0.35), residues: 344 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 0.658 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 81 average time/residue: 0.2036 time to fit residues: 20.9400 Evaluate side-chains 65 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 0.690 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0524 time to fit residues: 1.0949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 33 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 22 optimal weight: 0.0980 chunk 59 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.5865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 5432 Z= 0.177 Angle : 0.621 7.507 7396 Z= 0.304 Chirality : 0.047 0.133 896 Planarity : 0.004 0.044 972 Dihedral : 4.282 14.218 764 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer Outliers : 1.02 % 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: 0.25 (0.32), residues: 696 helix: 3.72 (0.58), residues: 64 sheet: -0.90 (0.29), residues: 288 loop : 0.68 (0.35), residues: 344 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 79 time to evaluate : 0.652 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 83 average time/residue: 0.1851 time to fit residues: 19.9462 Evaluate side-chains 69 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 0.641 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1389 time to fit residues: 1.4072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 34 optimal weight: 20.0000 chunk 63 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.6183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 5432 Z= 0.285 Angle : 0.701 7.573 7396 Z= 0.341 Chirality : 0.049 0.138 896 Planarity : 0.005 0.043 972 Dihedral : 4.581 14.898 764 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 1.70 % 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: 0.05 (0.33), residues: 696 helix: 3.73 (0.57), residues: 64 sheet: -1.17 (0.29), residues: 284 loop : 0.62 (0.35), residues: 348 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 70 time to evaluate : 0.673 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 76 average time/residue: 0.1837 time to fit residues: 18.2422 Evaluate side-chains 73 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 0.735 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0617 time to fit residues: 1.6209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 41 optimal weight: 0.2980 chunk 39 optimal weight: 3.9990 chunk 30 optimal weight: 0.0980 chunk 40 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 19 optimal weight: 7.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.6310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 5432 Z= 0.191 Angle : 0.632 6.889 7396 Z= 0.310 Chirality : 0.047 0.143 896 Planarity : 0.004 0.042 972 Dihedral : 4.325 15.777 764 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 0.51 % 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: 0.10 (0.33), residues: 696 helix: 3.92 (0.58), residues: 64 sheet: -1.20 (0.29), residues: 284 loop : 0.68 (0.35), residues: 348 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 77 time to evaluate : 0.673 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 79 average time/residue: 0.1974 time to fit residues: 19.8996 Evaluate side-chains 69 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 0.639 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0548 time to fit residues: 0.9528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 12 optimal weight: 8.9990 chunk 41 optimal weight: 20.0000 chunk 44 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.6451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 5432 Z= 0.254 Angle : 0.681 7.446 7396 Z= 0.330 Chirality : 0.048 0.135 896 Planarity : 0.005 0.042 972 Dihedral : 4.448 16.022 764 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer Outliers : 1.53 % 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 (0.33), residues: 696 helix: 3.90 (0.58), residues: 64 sheet: -1.27 (0.29), residues: 284 loop : 0.66 (0.35), residues: 348 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 0.687 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 79 average time/residue: 0.2085 time to fit residues: 20.8825 Evaluate side-chains 72 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.648 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0510 time to fit residues: 1.3255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 57 optimal weight: 20.0000 chunk 60 optimal weight: 3.9990 chunk 40 optimal weight: 0.3980 chunk 64 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.6583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 5432 Z= 0.180 Angle : 0.651 9.626 7396 Z= 0.315 Chirality : 0.047 0.135 896 Planarity : 0.004 0.041 972 Dihedral : 4.213 14.448 764 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer Outliers : 0.34 % 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: 0.12 (0.33), residues: 696 helix: 4.06 (0.58), residues: 64 sheet: -1.22 (0.29), residues: 284 loop : 0.70 (0.35), residues: 348 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 0.663 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 73 average time/residue: 0.1993 time to fit residues: 18.7434 Evaluate side-chains 64 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.663 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 67 optimal weight: 8.9990 chunk 62 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 41 optimal weight: 0.0670 chunk 33 optimal weight: 0.3980 chunk 42 optimal weight: 7.9990 chunk 57 optimal weight: 20.0000 chunk 16 optimal weight: 0.6980 chunk 49 optimal weight: 0.0980 chunk 7 optimal weight: 5.9990 overall best weight: 1.2520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.6664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 5432 Z= 0.178 Angle : 0.658 8.590 7396 Z= 0.318 Chirality : 0.047 0.142 896 Planarity : 0.004 0.040 972 Dihedral : 4.274 21.223 764 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer Outliers : 0.68 % 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: 0.25 (0.33), residues: 696 helix: 4.09 (0.59), residues: 64 sheet: -1.17 (0.30), residues: 284 loop : 0.84 (0.35), residues: 348 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 0.656 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 67 average time/residue: 0.1979 time to fit residues: 17.2183 Evaluate side-chains 63 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 0.681 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0527 time to fit residues: 1.1066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 14 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 6 optimal weight: 30.0000 chunk 9 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 3 optimal weight: 0.2980 chunk 39 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN C 117 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.077723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.063606 restraints weight = 11867.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.065767 restraints weight = 7318.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.067288 restraints weight = 5252.307| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.6751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 5432 Z= 0.283 Angle : 0.722 8.818 7396 Z= 0.345 Chirality : 0.049 0.146 896 Planarity : 0.004 0.041 972 Dihedral : 4.572 18.766 764 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 0.00 % 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 (0.33), residues: 696 helix: 3.92 (0.59), residues: 64 sheet: -1.21 (0.30), residues: 284 loop : 0.85 (0.35), residues: 348 =============================================================================== Job complete usr+sys time: 1316.68 seconds wall clock time: 24 minutes 23.27 seconds (1463.27 seconds total)