Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:14:09 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wlv_21843/11_2022/6wlv_21843.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wlv_21843/11_2022/6wlv_21843.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wlv_21843/11_2022/6wlv_21843.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wlv_21843/11_2022/6wlv_21843.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wlv_21843/11_2022/6wlv_21843.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wlv_21843/11_2022/6wlv_21843.pdb" } resolution = 3.45 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= 1.000 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 None 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: 4111 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2054 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain: "B" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2054 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.84, per 1000 atoms: 0.69 Number of scatterers: 4111 At special positions: 0 Unit cell: (94.371, 65.946, 78.453, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 3 19.00 S 14 16.00 O 682 8.00 N 668 7.00 C 2744 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS B 51 " distance=2.03 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: 1.86 Conformation dependent library (CDL) restraints added in 696.8 milliseconds 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 940 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 0 sheets defined 79.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 5 through 48 removed outlier: 3.812A pdb=" N THR A 9 " --> pdb=" O GLY A 5 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER A 10 " --> pdb=" O PRO A 6 " (cutoff:3.500A) Proline residue: A 29 - end of helix Processing helix chain 'A' and resid 53 through 70 removed outlier: 3.594A pdb=" N GLN A 70 " --> pdb=" O ASP A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 96 Processing helix chain 'A' and resid 108 through 152 removed outlier: 3.686A pdb=" N PHE A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Proline residue: A 124 - end of helix removed outlier: 3.677A pdb=" N ARG A 151 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 176 Processing helix chain 'A' and resid 177 through 186 removed outlier: 3.602A pdb=" N VAL A 181 " --> pdb=" O ILE A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 202 Processing helix chain 'A' and resid 222 through 243 Processing helix chain 'A' and resid 244 through 254 removed outlier: 4.442A pdb=" N MET A 248 " --> pdb=" O TRP A 244 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLU A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N HIS A 253 " --> pdb=" O PHE A 249 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS A 254 " --> pdb=" O VAL A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 259 removed outlier: 4.256A pdb=" N LYS A 258 " --> pdb=" O LYS A 254 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 254 through 259' Processing helix chain 'B' and resid 7 through 49 Proline residue: B 29 - end of helix removed outlier: 3.586A pdb=" N PHE B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 68 Processing helix chain 'B' and resid 69 through 71 No H-bonds generated for 'chain 'B' and resid 69 through 71' Processing helix chain 'B' and resid 84 through 96 removed outlier: 3.927A pdb=" N ILE B 90 " --> pdb=" O PRO B 86 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 93 " --> pdb=" O MET B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 152 Proline residue: B 124 - end of helix Processing helix chain 'B' and resid 157 through 176 Processing helix chain 'B' and resid 177 through 186 removed outlier: 3.724A pdb=" N VAL B 184 " --> pdb=" O PHE B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 202 Processing helix chain 'B' and resid 222 through 244 removed outlier: 3.710A pdb=" N LEU B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE B 241 " --> pdb=" O TRP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 254 Processing helix chain 'B' and resid 255 through 260 292 hydrogen bonds defined for protein. 876 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: 1.25 Time building geometry restraints manager: 1.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1226 1.34 - 1.46: 886 1.46 - 1.57: 2104 1.57 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 4236 Sorted by residual: bond pdb=" CB PRO B 179 " pdb=" CG PRO B 179 " ideal model delta sigma weight residual 1.492 1.453 0.039 5.00e-02 4.00e+02 6.15e-01 bond pdb=" CG1 ILE B 12 " pdb=" CD1 ILE B 12 " ideal model delta sigma weight residual 1.513 1.483 0.030 3.90e-02 6.57e+02 5.85e-01 bond pdb=" CB PRO A 179 " pdb=" CG PRO A 179 " ideal model delta sigma weight residual 1.492 1.455 0.037 5.00e-02 4.00e+02 5.57e-01 bond pdb=" CB ILE A 199 " pdb=" CG2 ILE A 199 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.28e-01 bond pdb=" C PRO B 178 " pdb=" N PRO B 179 " ideal model delta sigma weight residual 1.333 1.344 -0.010 1.44e-02 4.82e+03 5.14e-01 ... (remaining 4231 not shown) Histogram of bond angle deviations from ideal: 100.66 - 107.32: 147 107.32 - 113.99: 2373 113.99 - 120.66: 1894 120.66 - 127.33: 1288 127.33 - 133.99: 66 Bond angle restraints: 5768 Sorted by residual: angle pdb=" N PRO A 178 " pdb=" CA PRO A 178 " pdb=" C PRO A 178 " ideal model delta sigma weight residual 110.70 113.67 -2.97 1.22e+00 6.72e-01 5.93e+00 angle pdb=" N TRP B 85 " pdb=" CA TRP B 85 " pdb=" C TRP B 85 " ideal model delta sigma weight residual 109.81 114.30 -4.49 2.21e+00 2.05e-01 4.13e+00 angle pdb=" N PRO B 178 " pdb=" CA PRO B 178 " pdb=" C PRO B 178 " ideal model delta sigma weight residual 110.70 113.14 -2.44 1.22e+00 6.72e-01 3.98e+00 angle pdb=" C TRP B 244 " pdb=" N LYS B 245 " pdb=" CA LYS B 245 " ideal model delta sigma weight residual 120.79 123.55 -2.76 1.39e+00 5.18e-01 3.95e+00 angle pdb=" CA TRP B 85 " pdb=" C TRP B 85 " pdb=" N PRO B 86 " ideal model delta sigma weight residual 118.44 121.55 -3.11 1.59e+00 3.96e-01 3.83e+00 ... (remaining 5763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.04: 2142 16.04 - 32.08: 197 32.08 - 48.11: 52 48.11 - 64.15: 6 64.15 - 80.19: 2 Dihedral angle restraints: 2399 sinusoidal: 925 harmonic: 1474 Sorted by residual: dihedral pdb=" CB CYS A 51 " pdb=" SG CYS A 51 " pdb=" SG CYS B 51 " pdb=" CB CYS B 51 " ideal model delta sinusoidal sigma weight residual 93.00 134.32 -41.32 1 1.00e+01 1.00e-02 2.39e+01 dihedral pdb=" CA ASN A 189 " pdb=" C ASN A 189 " pdb=" N TYR A 190 " pdb=" CA TYR A 190 " ideal model delta harmonic sigma weight residual -180.00 -163.83 -16.17 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA GLY A 102 " pdb=" C GLY A 102 " pdb=" N ASN A 103 " pdb=" CA ASN A 103 " ideal model delta harmonic sigma weight residual 180.00 164.16 15.84 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 2396 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 333 0.026 - 0.052: 189 0.052 - 0.079: 77 0.079 - 0.105: 33 0.105 - 0.131: 6 Chirality restraints: 638 Sorted by residual: chirality pdb=" CB VAL A 246 " pdb=" CA VAL A 246 " pdb=" CG1 VAL A 246 " pdb=" CG2 VAL A 246 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CA PRO A 179 " pdb=" N PRO A 179 " pdb=" C PRO A 179 " pdb=" CB PRO A 179 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 3.94e-01 chirality pdb=" CA THR A 98 " pdb=" N THR A 98 " pdb=" C THR A 98 " pdb=" CB THR A 98 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.12 2.00e-01 2.50e+01 3.59e-01 ... (remaining 635 not shown) Planarity restraints: 706 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 178 " -0.027 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO A 179 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 179 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 179 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 178 " 0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO B 179 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 179 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 179 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 177 " 0.017 5.00e-02 4.00e+02 2.51e-02 1.01e+00 pdb=" N PRO A 178 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO A 178 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 178 " 0.014 5.00e-02 4.00e+02 ... (remaining 703 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.80: 1122 2.80 - 3.38: 4936 3.38 - 3.97: 7710 3.97 - 4.55: 10811 4.55 - 5.14: 15422 Nonbonded interactions: 40001 Sorted by model distance: nonbonded pdb=" O ALA A 93 " pdb=" OG1 THR A 97 " model vdw 2.211 2.440 nonbonded pdb=" O LEU A 7 " pdb=" OG SER A 10 " model vdw 2.214 2.440 nonbonded pdb=" O GLU B 33 " pdb=" ND2 ASN B 37 " model vdw 2.284 2.520 nonbonded pdb=" NE2 GLN A 54 " pdb=" OD1 ASP A 58 " model vdw 2.321 2.520 nonbonded pdb=" O ALA B 236 " pdb=" OG SER B 239 " model vdw 2.357 2.440 ... (remaining 39996 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' and resid 5 through 260) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 3 8.98 5 S 14 5.16 5 C 2744 2.51 5 N 668 2.21 5 O 682 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: 0.160 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: 0.000 Extract box with map and model: 1.270 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.040 Process input model: 15.970 Find NCS groups from input model: 0.230 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 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 : 0.004 0.039 4236 Z= 0.250 Angle : 0.558 5.404 5768 Z= 0.318 Chirality : 0.040 0.131 638 Planarity : 0.003 0.040 706 Dihedral : 13.212 80.190 1456 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % 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: -0.61 (0.36), residues: 508 helix: 0.28 (0.25), residues: 372 sheet: None (None), residues: 0 loop : -2.17 (0.54), residues: 136 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.496 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1752 time to fit residues: 17.3629 Evaluate side-chains 55 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.439 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 0.0020 chunk 20 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 15 optimal weight: 30.0000 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 253 HIS B 174 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 4236 Z= 0.197 Angle : 0.540 5.746 5768 Z= 0.281 Chirality : 0.040 0.125 638 Planarity : 0.004 0.049 706 Dihedral : 3.766 14.259 552 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer Outliers : 1.41 % 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: 1.14 (0.38), residues: 508 helix: 1.71 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -2.59 (0.53), residues: 119 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 72 average time/residue: 0.1447 time to fit residues: 13.4828 Evaluate side-chains 65 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 60 time to evaluate : 0.487 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0403 time to fit residues: 1.0136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 4.9990 chunk 14 optimal weight: 20.0000 chunk 37 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 45 optimal weight: 0.0030 chunk 49 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 4236 Z= 0.218 Angle : 0.530 5.517 5768 Z= 0.276 Chirality : 0.040 0.127 638 Planarity : 0.004 0.051 706 Dihedral : 3.690 13.437 552 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer Outliers : 0.70 % 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: 1.72 (0.39), residues: 508 helix: 2.12 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -2.34 (0.54), residues: 120 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 69 average time/residue: 0.1506 time to fit residues: 13.3754 Evaluate side-chains 64 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 0.488 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0511 time to fit residues: 0.7346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 13 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 4236 Z= 0.218 Angle : 0.520 6.782 5768 Z= 0.270 Chirality : 0.040 0.134 638 Planarity : 0.004 0.052 706 Dihedral : 3.650 13.754 552 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer Outliers : 1.64 % 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: 1.99 (0.39), residues: 508 helix: 2.32 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -2.23 (0.55), residues: 120 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 71 average time/residue: 0.1336 time to fit residues: 12.6073 Evaluate side-chains 65 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 0.542 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0425 time to fit residues: 0.8102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 41 optimal weight: 0.0980 chunk 33 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 43 optimal weight: 0.3980 chunk 12 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 4236 Z= 0.162 Angle : 0.511 6.169 5768 Z= 0.261 Chirality : 0.039 0.160 638 Planarity : 0.004 0.053 706 Dihedral : 3.559 13.222 552 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.39), residues: 508 helix: 2.49 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -2.22 (0.54), residues: 119 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 71 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 77 average time/residue: 0.1384 time to fit residues: 14.0095 Evaluate side-chains 69 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 0.569 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0464 time to fit residues: 1.0266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 4236 Z= 0.169 Angle : 0.514 7.011 5768 Z= 0.265 Chirality : 0.039 0.140 638 Planarity : 0.004 0.054 706 Dihedral : 3.506 12.908 552 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.39), residues: 508 helix: 2.55 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -2.22 (0.53), residues: 120 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 70 average time/residue: 0.1361 time to fit residues: 12.5469 Evaluate side-chains 63 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 0.464 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0460 time to fit residues: 0.6977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.0030 chunk 40 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 9 optimal weight: 0.0980 chunk 32 optimal weight: 5.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 4236 Z= 0.151 Angle : 0.509 6.660 5768 Z= 0.261 Chirality : 0.038 0.153 638 Planarity : 0.004 0.054 706 Dihedral : 3.418 12.854 552 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.39), residues: 508 helix: 2.61 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -2.18 (0.52), residues: 120 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 74 average time/residue: 0.1257 time to fit residues: 12.5213 Evaluate side-chains 66 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 0.491 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0522 time to fit residues: 0.7290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 0.2980 chunk 19 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 13 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 4236 Z= 0.171 Angle : 0.524 7.319 5768 Z= 0.271 Chirality : 0.039 0.144 638 Planarity : 0.004 0.054 706 Dihedral : 3.467 12.983 552 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.38), residues: 508 helix: 2.62 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -2.09 (0.53), residues: 120 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 70 average time/residue: 0.1283 time to fit residues: 12.0754 Evaluate side-chains 65 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 0.494 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0421 time to fit residues: 0.7985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 5.9990 chunk 42 optimal weight: 0.0870 chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 0.0050 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 49 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 overall best weight: 0.7974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 4236 Z= 0.168 Angle : 0.533 6.992 5768 Z= 0.275 Chirality : 0.039 0.151 638 Planarity : 0.004 0.054 706 Dihedral : 3.454 12.939 552 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.38), residues: 508 helix: 2.64 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -2.11 (0.52), residues: 120 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 66 average time/residue: 0.1232 time to fit residues: 11.0224 Evaluate side-chains 64 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.517 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 39 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 4236 Z= 0.268 Angle : 0.565 8.606 5768 Z= 0.291 Chirality : 0.041 0.185 638 Planarity : 0.004 0.054 706 Dihedral : 3.566 13.462 552 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.38), residues: 508 helix: 2.57 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -2.14 (0.53), residues: 120 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 66 average time/residue: 0.1372 time to fit residues: 11.9555 Evaluate side-chains 65 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 0.494 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0485 time to fit residues: 0.8298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 7 optimal weight: 0.0370 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.7862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.103873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.080371 restraints weight = 10293.500| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.61 r_work: 0.3190 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work: 0.3169 rms_B_bonded: 2.39 restraints_weight: 0.1250 r_work: 0.3158 rms_B_bonded: 2.48 restraints_weight: 0.0625 r_work: 0.3146 rms_B_bonded: 2.61 restraints_weight: 0.0312 r_work: 0.3133 rms_B_bonded: 2.78 restraints_weight: 0.0156 r_work: 0.3120 rms_B_bonded: 2.98 restraints_weight: 0.0078 r_work: 0.3105 rms_B_bonded: 3.22 restraints_weight: 0.0039 r_work: 0.3090 rms_B_bonded: 3.50 restraints_weight: 0.0020 r_work: 0.3074 rms_B_bonded: 3.82 restraints_weight: 0.0010 r_work: 0.3056 rms_B_bonded: 4.19 restraints_weight: 0.0005 r_work: 0.3038 rms_B_bonded: 4.60 restraints_weight: 0.0002 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 4236 Z= 0.163 Angle : 0.541 8.027 5768 Z= 0.276 Chirality : 0.040 0.241 638 Planarity : 0.004 0.054 706 Dihedral : 3.470 12.883 552 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % 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: 2.45 (0.38), residues: 508 helix: 2.62 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -2.03 (0.53), residues: 119 =============================================================================== Job complete usr+sys time: 1052.89 seconds wall clock time: 20 minutes 14.48 seconds (1214.48 seconds total)