Starting phenix.real_space_refine on Thu Dec 7 15:48:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r23_4708/12_2023/6r23_4708.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r23_4708/12_2023/6r23_4708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r23_4708/12_2023/6r23_4708.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r23_4708/12_2023/6r23_4708.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r23_4708/12_2023/6r23_4708.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r23_4708/12_2023/6r23_4708.pdb" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.026 sd= 0.295 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 974 2.51 5 N 260 2.21 5 O 274 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 122": "OE1" <-> "OE2" Residue "A PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 173": "OE1" <-> "OE2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 122": "OE1" <-> "OE2" Residue "B PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 173": "OE1" <-> "OE2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "B TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 1518 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 759 Classifications: {'peptide': 91} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 83} Chain: "B" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 759 Classifications: {'peptide': 91} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 83} Time building chain proxies: 1.54, per 1000 atoms: 1.01 Number of scatterers: 1518 At special positions: 0 Unit cell: (90.72, 56.16, 47.52, 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 10 16.00 O 274 8.00 N 260 7.00 C 974 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 295.8 milliseconds 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 356 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 0 sheets defined 68.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 109 through 119 removed outlier: 4.046A pdb=" N ILE A 113 " --> pdb=" O ASP A 109 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR A 118 " --> pdb=" O PHE A 114 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 139 removed outlier: 4.323A pdb=" N ARG A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU A 130 " --> pdb=" O GLY A 126 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP A 139 " --> pdb=" O ARG A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 157 removed outlier: 3.775A pdb=" N TYR A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 169 removed outlier: 3.743A pdb=" N MET A 169 " --> pdb=" O ASN A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 188 removed outlier: 3.545A pdb=" N THR A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 119 removed outlier: 4.046A pdb=" N ILE B 113 " --> pdb=" O ASP B 109 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR B 118 " --> pdb=" O PHE B 114 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 139 removed outlier: 4.322A pdb=" N ARG B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU B 130 " --> pdb=" O GLY B 126 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP B 139 " --> pdb=" O ARG B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 157 removed outlier: 3.775A pdb=" N TYR B 155 " --> pdb=" O ALA B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 169 removed outlier: 3.743A pdb=" N MET B 169 " --> pdb=" O ASN B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 188 removed outlier: 3.546A pdb=" N THR B 185 " --> pdb=" O GLU B 181 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) 64 hydrogen bonds defined for protein. 192 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.34 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 480 1.34 - 1.46: 268 1.46 - 1.57: 784 1.57 - 1.69: 0 1.69 - 1.80: 20 Bond restraints: 1552 Sorted by residual: bond pdb=" C ASP B 144 " pdb=" N PHE B 145 " ideal model delta sigma weight residual 1.332 1.350 -0.017 1.40e-02 5.10e+03 1.52e+00 bond pdb=" C ASP A 144 " pdb=" N PHE A 145 " ideal model delta sigma weight residual 1.332 1.349 -0.017 1.40e-02 5.10e+03 1.48e+00 bond pdb=" N PHE A 145 " pdb=" CA PHE A 145 " ideal model delta sigma weight residual 1.457 1.473 -0.015 1.29e-02 6.01e+03 1.39e+00 bond pdb=" N PHE B 145 " pdb=" CA PHE B 145 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.34e+00 bond pdb=" C PRO B 142 " pdb=" N PRO B 143 " ideal model delta sigma weight residual 1.334 1.307 0.027 2.34e-02 1.83e+03 1.29e+00 ... (remaining 1547 not shown) Histogram of bond angle deviations from ideal: 99.44 - 106.33: 54 106.33 - 113.22: 826 113.22 - 120.11: 541 120.11 - 127.00: 651 127.00 - 133.89: 20 Bond angle restraints: 2092 Sorted by residual: angle pdb=" C ARG B 140 " pdb=" N MET B 141 " pdb=" CA MET B 141 " ideal model delta sigma weight residual 121.80 129.75 -7.95 2.44e+00 1.68e-01 1.06e+01 angle pdb=" C ARG A 140 " pdb=" N MET A 141 " pdb=" CA MET A 141 " ideal model delta sigma weight residual 121.80 129.72 -7.92 2.44e+00 1.68e-01 1.05e+01 angle pdb=" C ASP B 144 " pdb=" N PHE B 145 " pdb=" CA PHE B 145 " ideal model delta sigma weight residual 121.54 127.72 -6.18 1.91e+00 2.74e-01 1.05e+01 angle pdb=" C ASP A 144 " pdb=" N PHE A 145 " pdb=" CA PHE A 145 " ideal model delta sigma weight residual 121.54 127.71 -6.17 1.91e+00 2.74e-01 1.04e+01 angle pdb=" N SER B 121 " pdb=" CA SER B 121 " pdb=" C SER B 121 " ideal model delta sigma weight residual 108.24 112.30 -4.06 1.32e+00 5.74e-01 9.45e+00 ... (remaining 2087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 820 16.66 - 33.32: 112 33.32 - 49.98: 28 49.98 - 66.63: 0 66.63 - 83.29: 6 Dihedral angle restraints: 966 sinusoidal: 422 harmonic: 544 Sorted by residual: dihedral pdb=" CA ARG B 191 " pdb=" C ARG B 191 " pdb=" N PHE B 192 " pdb=" CA PHE B 192 " ideal model delta harmonic sigma weight residual 180.00 142.43 37.57 0 5.00e+00 4.00e-02 5.65e+01 dihedral pdb=" CA ARG A 191 " pdb=" C ARG A 191 " pdb=" N PHE A 192 " pdb=" CA PHE A 192 " ideal model delta harmonic sigma weight residual 180.00 142.44 37.56 0 5.00e+00 4.00e-02 5.64e+01 dihedral pdb=" CA MET B 141 " pdb=" C MET B 141 " pdb=" N PRO B 142 " pdb=" CA PRO B 142 " ideal model delta harmonic sigma weight residual 180.00 149.42 30.58 0 5.00e+00 4.00e-02 3.74e+01 ... (remaining 963 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.034: 148 0.034 - 0.068: 56 0.068 - 0.102: 14 0.102 - 0.136: 4 0.136 - 0.169: 6 Chirality restraints: 228 Sorted by residual: chirality pdb=" CA PRO A 108 " pdb=" N PRO A 108 " pdb=" C PRO A 108 " pdb=" CB PRO A 108 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.17e-01 chirality pdb=" CA PRO B 108 " pdb=" N PRO B 108 " pdb=" C PRO B 108 " pdb=" CB PRO B 108 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.02e-01 chirality pdb=" CB ILE A 127 " pdb=" CA ILE A 127 " pdb=" CG1 ILE A 127 " pdb=" CG2 ILE A 127 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.52e-01 ... (remaining 225 not shown) Planarity restraints: 266 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 106 " -0.028 5.00e-02 4.00e+02 4.17e-02 2.79e+00 pdb=" N PRO A 107 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 107 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 107 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 106 " -0.027 5.00e-02 4.00e+02 4.15e-02 2.75e+00 pdb=" N PRO B 107 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 107 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 107 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 166 " -0.007 2.00e-02 2.50e+03 1.43e-02 2.05e+00 pdb=" C ILE A 166 " 0.025 2.00e-02 2.50e+03 pdb=" O ILE A 166 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL A 167 " -0.008 2.00e-02 2.50e+03 ... (remaining 263 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 491 2.85 - 3.36: 1529 3.36 - 3.87: 2170 3.87 - 4.39: 2419 4.39 - 4.90: 3859 Nonbonded interactions: 10468 Sorted by model distance: nonbonded pdb=" O ILE B 152 " pdb=" OG1 THR B 156 " model vdw 2.332 2.440 nonbonded pdb=" O ILE A 152 " pdb=" OG1 THR A 156 " model vdw 2.333 2.440 nonbonded pdb=" O PHE A 114 " pdb=" OG1 THR A 118 " model vdw 2.353 2.440 nonbonded pdb=" O PHE B 114 " pdb=" OG1 THR B 118 " model vdw 2.353 2.440 nonbonded pdb=" OE1 GLU A 122 " pdb=" OG1 THR A 160 " model vdw 2.395 2.440 ... (remaining 10463 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' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' } Set refine NCS operators NCS operators will be refined. 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 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: 0.240 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: 0.860 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.880 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.000 Set refine NCS operators: 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 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 : 0.006 0.029 1552 Z= 0.368 Angle : 1.069 7.947 2092 Z= 0.635 Chirality : 0.046 0.169 228 Planarity : 0.007 0.042 266 Dihedral : 16.555 83.293 610 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.00 % Allowed : 12.20 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.19 % Twisted Proline : 16.67 % Twisted General : 1.19 % 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: -4.61 (0.51), residues: 178 helix: -3.06 (0.33), residues: 100 sheet: None (None), residues: 0 loop : -2.93 (0.71), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 138 HIS 0.004 0.002 HIS A 170 PHE 0.023 0.003 PHE B 145 TYR 0.009 0.002 TYR A 164 ARG 0.004 0.001 ARG B 191 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 82 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.099 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.2272 time to fit residues: 5.9704 Evaluate side-chains 11 residues out of total 82 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.084 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 0.0570 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 5 optimal weight: 0.0170 chunk 8 optimal weight: 10.0000 chunk 10 optimal weight: 0.3980 chunk 16 optimal weight: 0.7980 chunk 11 optimal weight: 0.3980 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 1552 Z= 0.192 Angle : 0.712 6.183 2092 Z= 0.360 Chirality : 0.036 0.107 228 Planarity : 0.005 0.025 266 Dihedral : 6.043 25.597 202 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 1.12 % Allowed : 5.62 % Favored : 93.26 % Rotamer: Outliers : 1.22 % Allowed : 1.22 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.19 % 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: -1.94 (0.62), residues: 178 helix: -0.72 (0.45), residues: 104 sheet: None (None), residues: 0 loop : -2.04 (0.81), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 138 HIS 0.001 0.000 HIS B 170 PHE 0.019 0.003 PHE A 114 TYR 0.005 0.001 TYR B 183 ARG 0.003 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 82 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.101 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 24 average time/residue: 0.1339 time to fit residues: 3.5444 Evaluate side-chains 10 residues out of total 82 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.088 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 5 optimal weight: 0.0570 chunk 13 optimal weight: 0.7980 chunk 12 optimal weight: 0.0020 chunk 8 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 0.1980 overall best weight: 0.4108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.5191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 1552 Z= 0.181 Angle : 0.621 6.059 2092 Z= 0.311 Chirality : 0.037 0.128 228 Planarity : 0.003 0.022 266 Dihedral : 4.984 23.042 202 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.19 % 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: -0.59 (0.68), residues: 178 helix: 0.57 (0.52), residues: 106 sheet: None (None), residues: 0 loop : -1.89 (0.85), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 138 HIS 0.001 0.001 HIS B 170 PHE 0.013 0.002 PHE B 192 TYR 0.009 0.001 TYR A 155 ARG 0.003 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 82 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.098 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1574 time to fit residues: 2.6119 Evaluate side-chains 10 residues out of total 82 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.098 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 16 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 12 optimal weight: 0.0070 chunk 7 optimal weight: 4.9990 chunk 5 optimal weight: 0.4980 overall best weight: 1.2400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.6127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 1552 Z= 0.194 Angle : 0.590 4.411 2092 Z= 0.295 Chirality : 0.037 0.128 228 Planarity : 0.004 0.017 266 Dihedral : 4.941 19.365 202 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 1.12 % Allowed : 6.74 % Favored : 92.13 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.19 % 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 (0.69), residues: 178 helix: 0.84 (0.52), residues: 106 sheet: None (None), residues: 0 loop : -1.80 (0.86), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 138 HIS 0.001 0.001 HIS A 170 PHE 0.013 0.002 PHE A 145 TYR 0.012 0.002 TYR A 183 ARG 0.002 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 82 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.103 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.1408 time to fit residues: 2.0749 Evaluate side-chains 10 residues out of total 82 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.098 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 10.0000 chunk 14 optimal weight: 0.0770 chunk 8 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 5 optimal weight: 0.0020 chunk 9 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 overall best weight: 0.4946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.6446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 1552 Z= 0.190 Angle : 0.604 5.854 2092 Z= 0.293 Chirality : 0.035 0.109 228 Planarity : 0.003 0.018 266 Dihedral : 4.670 16.139 202 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 1.12 % Allowed : 4.49 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.19 % 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 (0.69), residues: 178 helix: 0.79 (0.51), residues: 106 sheet: None (None), residues: 0 loop : -1.63 (0.90), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 138 HIS 0.000 0.000 HIS B 170 PHE 0.011 0.001 PHE B 145 TYR 0.019 0.002 TYR A 155 ARG 0.002 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 82 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.101 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.1370 time to fit residues: 2.0288 Evaluate side-chains 9 residues out of total 82 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 9 time to evaluate : 0.099 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 0.0570 chunk 9 optimal weight: 6.9990 chunk 12 optimal weight: 0.6980 chunk 14 optimal weight: 0.1980 chunk 17 optimal weight: 9.9990 chunk 10 optimal weight: 0.0570 chunk 8 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 overall best weight: 0.2816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.6859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 1552 Z= 0.185 Angle : 0.568 5.953 2092 Z= 0.274 Chirality : 0.034 0.100 228 Planarity : 0.003 0.016 266 Dihedral : 4.193 14.629 202 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.19 % 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: -0.17 (0.69), residues: 178 helix: 0.87 (0.51), residues: 106 sheet: None (None), residues: 0 loop : -1.63 (0.89), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 138 HIS 0.000 0.000 HIS A 170 PHE 0.007 0.001 PHE A 145 TYR 0.016 0.002 TYR A 183 ARG 0.002 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 82 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.097 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1285 time to fit residues: 2.1817 Evaluate side-chains 12 residues out of total 82 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.097 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 11 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 1 optimal weight: 0.0980 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 0.0050 chunk 16 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 12 optimal weight: 0.0670 chunk 4 optimal weight: 0.1980 chunk 14 optimal weight: 2.9990 overall best weight: 0.4734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.6995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 1552 Z= 0.177 Angle : 0.559 5.184 2092 Z= 0.269 Chirality : 0.034 0.089 228 Planarity : 0.003 0.019 266 Dihedral : 4.120 13.350 202 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.19 % 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: 0.01 (0.70), residues: 178 helix: 1.03 (0.52), residues: 106 sheet: None (None), residues: 0 loop : -1.58 (0.89), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 138 HIS 0.000 0.000 HIS A 170 PHE 0.008 0.001 PHE B 145 TYR 0.015 0.002 TYR A 183 ARG 0.002 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 82 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.097 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1636 time to fit residues: 2.8740 Evaluate side-chains 12 residues out of total 82 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.097 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 17 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 0.2980 chunk 1 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.6950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 1552 Z= 0.187 Angle : 0.599 6.890 2092 Z= 0.287 Chirality : 0.034 0.109 228 Planarity : 0.004 0.023 266 Dihedral : 4.085 11.865 202 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.19 % 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 (0.71), residues: 178 helix: 1.21 (0.53), residues: 106 sheet: None (None), residues: 0 loop : -1.54 (0.91), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 138 HIS 0.001 0.001 HIS A 170 PHE 0.007 0.001 PHE B 114 TYR 0.015 0.002 TYR B 155 ARG 0.003 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 82 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.099 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1149 time to fit residues: 1.9767 Evaluate side-chains 11 residues out of total 82 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.098 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 1 optimal weight: 0.0570 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 10 optimal weight: 0.0570 chunk 16 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.7185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 1552 Z= 0.181 Angle : 0.556 5.199 2092 Z= 0.269 Chirality : 0.034 0.100 228 Planarity : 0.004 0.019 266 Dihedral : 4.014 12.596 202 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.71), residues: 178 helix: 1.10 (0.53), residues: 106 sheet: None (None), residues: 0 loop : -1.46 (0.92), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 138 HIS 0.000 0.000 HIS B 170 PHE 0.009 0.001 PHE B 114 TYR 0.016 0.001 TYR A 183 ARG 0.003 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 82 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.091 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.2655 time to fit residues: 4.4224 Evaluate side-chains 12 residues out of total 82 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.263 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 3 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 4 optimal weight: 0.4980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.6980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 1552 Z= 0.198 Angle : 0.622 7.069 2092 Z= 0.297 Chirality : 0.034 0.098 228 Planarity : 0.004 0.026 266 Dihedral : 4.034 12.070 202 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.19 % 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: 0.13 (0.72), residues: 178 helix: 1.17 (0.53), residues: 106 sheet: None (None), residues: 0 loop : -1.62 (0.91), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 138 HIS 0.001 0.001 HIS B 170 PHE 0.007 0.001 PHE A 145 TYR 0.013 0.002 TYR B 155 ARG 0.002 0.000 ARG B 135 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 82 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.110 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.1269 time to fit residues: 2.0269 Evaluate side-chains 11 residues out of total 82 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.096 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.066469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.060763 restraints weight = 3974.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.061987 restraints weight = 2477.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.062864 restraints weight = 1687.839| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.7006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 1552 Z= 0.201 Angle : 0.571 4.578 2092 Z= 0.285 Chirality : 0.035 0.101 228 Planarity : 0.004 0.024 266 Dihedral : 4.300 12.524 202 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.19 % 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: -0.07 (0.71), residues: 178 helix: 0.87 (0.52), residues: 106 sheet: None (None), residues: 0 loop : -1.44 (0.92), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 138 HIS 0.001 0.001 HIS A 170 PHE 0.014 0.002 PHE B 114 TYR 0.012 0.001 TYR B 183 ARG 0.001 0.000 ARG A 135 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 830.47 seconds wall clock time: 20 minutes 34.42 seconds (1234.42 seconds total)