Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 2 16:29:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7og6_12879/10_2023/7og6_12879.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7og6_12879/10_2023/7og6_12879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7og6_12879/10_2023/7og6_12879.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7og6_12879/10_2023/7og6_12879.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7og6_12879/10_2023/7og6_12879.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7og6_12879/10_2023/7og6_12879.pdb" } resolution = 3.3 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= 0.002 sd= 0.018 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: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 4 5.16 5 C 996 2.51 5 N 265 2.21 5 O 332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 11": "OE1" <-> "OE2" Residue "A GLU 54": "OE1" <-> "OE2" Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 61": "OD1" <-> "OD2" Residue "A GLU 78": "OE1" <-> "OE2" Residue "A ARG 100": "NH1" <-> "NH2" Residue "A PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 110": "NH1" <-> "NH2" Residue "A ASP 112": "OD1" <-> "OD2" Residue "A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 137": "OD1" <-> "OD2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A ARG 160": "NH1" <-> "NH2" Residue "A PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 1602 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1502 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 183} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Time building chain proxies: 1.53, per 1000 atoms: 0.96 Number of scatterers: 1602 At special positions: 0 Unit cell: (69.225, 71.355, 68.16, 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) S 4 16.00 P 5 15.00 O 332 8.00 N 265 7.00 C 996 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: 0.74 Conformation dependent library (CDL) restraints added in 232.8 milliseconds 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 382 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 0 sheets defined 43.7% alpha, 0.0% beta 0 base pairs and 1 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 31 through 40 removed outlier: 3.613A pdb=" N ALA A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU A 37 " --> pdb=" O THR A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 63 removed outlier: 3.713A pdb=" N ALA A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE A 58 " --> pdb=" O GLU A 54 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP A 61 " --> pdb=" O ASN A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 89 Processing helix chain 'A' and resid 94 through 111 removed outlier: 3.776A pdb=" N PHE A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE A 102 " --> pdb=" O PHE A 98 " (cutoff:3.500A) Proline residue: A 104 - end of helix removed outlier: 3.715A pdb=" N ASN A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 132 removed outlier: 3.853A pdb=" N LYS A 129 " --> pdb=" O PRO A 126 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N PHE A 130 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA A 131 " --> pdb=" O GLU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.556A pdb=" N VAL A 139 " --> pdb=" O PHE A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 175 removed outlier: 3.521A pdb=" N VAL A 169 " --> pdb=" O THR A 165 " (cutoff:3.500A) 45 hydrogen bonds defined for protein. 126 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 1 stacking parallelities Total time for adding SS restraints: 0.31 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 484 1.33 - 1.45: 276 1.45 - 1.57: 871 1.57 - 1.69: 9 1.69 - 1.81: 6 Bond restraints: 1646 Sorted by residual: bond pdb=" C ASN A 141 " pdb=" O ASN A 141 " ideal model delta sigma weight residual 1.249 1.234 0.015 8.50e-03 1.38e+04 3.16e+00 bond pdb=" C MET A 145 " pdb=" N GLN A 146 " ideal model delta sigma weight residual 1.339 1.248 0.092 5.57e-02 3.22e+02 2.71e+00 bond pdb=" CA LYS A 89 " pdb=" CB LYS A 89 " ideal model delta sigma weight residual 1.526 1.503 0.023 1.51e-02 4.39e+03 2.24e+00 bond pdb=" C LYS A 125 " pdb=" N PRO A 126 " ideal model delta sigma weight residual 1.335 1.319 0.016 1.19e-02 7.06e+03 1.82e+00 bond pdb=" CG GLU A 120 " pdb=" CD GLU A 120 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.76e+00 ... (remaining 1641 not shown) Histogram of bond angle deviations from ideal: 100.95 - 107.54: 94 107.54 - 114.13: 936 114.13 - 120.72: 677 120.72 - 127.31: 544 127.31 - 133.90: 17 Bond angle restraints: 2268 Sorted by residual: angle pdb=" N GLN A 173 " pdb=" CA GLN A 173 " pdb=" C GLN A 173 " ideal model delta sigma weight residual 114.62 106.03 8.59 1.14e+00 7.69e-01 5.68e+01 angle pdb=" N VAL A 84 " pdb=" CA VAL A 84 " pdb=" C VAL A 84 " ideal model delta sigma weight residual 111.45 107.42 4.03 9.30e-01 1.16e+00 1.88e+01 angle pdb=" N GLU A 140 " pdb=" CA GLU A 140 " pdb=" C GLU A 140 " ideal model delta sigma weight residual 113.21 108.38 4.83 1.15e+00 7.56e-01 1.76e+01 angle pdb=" N ASN A 14 " pdb=" CA ASN A 14 " pdb=" C ASN A 14 " ideal model delta sigma weight residual 114.31 109.25 5.06 1.29e+00 6.01e-01 1.54e+01 angle pdb=" N ILE A 200 " pdb=" CA ILE A 200 " pdb=" C ILE A 200 " ideal model delta sigma weight residual 113.43 109.17 4.26 1.09e+00 8.42e-01 1.53e+01 ... (remaining 2263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 852 17.04 - 34.08: 93 34.08 - 51.12: 26 51.12 - 68.16: 9 68.16 - 85.21: 5 Dihedral angle restraints: 985 sinusoidal: 403 harmonic: 582 Sorted by residual: dihedral pdb=" CA PRO A 198 " pdb=" C PRO A 198 " pdb=" N THR A 199 " pdb=" CA THR A 199 " ideal model delta harmonic sigma weight residual 180.00 148.52 31.48 0 5.00e+00 4.00e-02 3.96e+01 dihedral pdb=" CA PHE A 172 " pdb=" C PHE A 172 " pdb=" N GLN A 173 " pdb=" CA GLN A 173 " ideal model delta harmonic sigma weight residual 180.00 163.69 16.31 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA PHE A 5 " pdb=" C PHE A 5 " pdb=" N PRO A 6 " pdb=" CA PRO A 6 " ideal model delta harmonic sigma weight residual -180.00 -164.48 -15.52 0 5.00e+00 4.00e-02 9.63e+00 ... (remaining 982 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 130 0.027 - 0.055: 84 0.055 - 0.082: 39 0.082 - 0.109: 11 0.109 - 0.137: 6 Chirality restraints: 270 Sorted by residual: chirality pdb=" CA PRO A 6 " pdb=" N PRO A 6 " pdb=" C PRO A 6 " pdb=" CB PRO A 6 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.67e-01 chirality pdb=" CA PRO A 126 " pdb=" N PRO A 126 " pdb=" C PRO A 126 " pdb=" CB PRO A 126 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.82e-01 chirality pdb=" CA PHE A 135 " pdb=" N PHE A 135 " pdb=" C PHE A 135 " pdb=" CB PHE A 135 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.42e-01 ... (remaining 267 not shown) Planarity restraints: 284 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 197 " 0.053 5.00e-02 4.00e+02 8.09e-02 1.05e+01 pdb=" N PRO A 198 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 198 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 198 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 147 " 0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO A 148 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 148 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 148 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 135 " 0.009 2.00e-02 2.50e+03 8.99e-03 1.42e+00 pdb=" CG PHE A 135 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE A 135 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE A 135 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 135 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 135 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 135 " 0.000 2.00e-02 2.50e+03 ... (remaining 281 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 618 2.84 - 3.35: 1561 3.35 - 3.87: 2505 3.87 - 4.38: 2985 4.38 - 4.90: 4693 Nonbonded interactions: 12362 Sorted by model distance: nonbonded pdb=" O ALA A 90 " pdb=" OG SER A 91 " model vdw 2.325 2.440 nonbonded pdb=" O ASP A 61 " pdb=" ND2 ASN A 118 " model vdw 2.329 2.520 nonbonded pdb=" O SER A 185 " pdb=" OG1 THR A 189 " model vdw 2.332 2.440 nonbonded pdb=" NH2 ARG A 96 " pdb=" OP2 U R 44 " model vdw 2.356 2.520 nonbonded pdb=" N ASP A 134 " pdb=" OD1 ASP A 134 " model vdw 2.402 2.520 ... (remaining 12357 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.870 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.260 Find NCS groups from input model: 0.210 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 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 : 0.008 0.092 1646 Z= 0.502 Angle : 0.816 8.590 2268 Z= 0.540 Chirality : 0.044 0.137 270 Planarity : 0.006 0.081 284 Dihedral : 17.328 85.206 603 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 6.10 % Allowed : 20.12 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.55 % 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: -4.47 (0.46), residues: 197 helix: -3.17 (0.38), residues: 88 sheet: None (None), residues: 0 loop : -2.84 (0.49), residues: 109 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 15 time to evaluate : 0.176 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 25 average time/residue: 0.0903 time to fit residues: 2.8511 Evaluate side-chains 10 residues out of total 165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 7 time to evaluate : 0.181 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0207 time to fit residues: 0.3360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 16 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 11 optimal weight: 40.0000 chunk 17 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 15 optimal weight: 30.0000 chunk 13 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 30 GLN A 83 GLN A 146 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1646 Z= 0.211 Angle : 0.586 5.500 2268 Z= 0.301 Chirality : 0.041 0.134 270 Planarity : 0.006 0.071 284 Dihedral : 10.304 79.351 262 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.05 % Allowed : 22.56 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.54), residues: 197 helix: -1.98 (0.52), residues: 86 sheet: None (None), residues: 0 loop : -2.26 (0.54), residues: 111 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 9 time to evaluate : 0.178 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 14 average time/residue: 0.0833 time to fit residues: 1.6215 Evaluate side-chains 8 residues out of total 165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 7 time to evaluate : 0.188 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0210 time to fit residues: 0.2685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 17 optimal weight: 0.2980 chunk 12 optimal weight: 8.9990 chunk 8 optimal weight: 40.0000 chunk 1 optimal weight: 50.0000 chunk 11 optimal weight: 8.9990 chunk 18 optimal weight: 20.0000 chunk 9 optimal weight: 20.0000 chunk 16 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 overall best weight: 6.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 1646 Z= 0.208 Angle : 0.537 4.659 2268 Z= 0.280 Chirality : 0.040 0.130 270 Planarity : 0.005 0.063 284 Dihedral : 9.978 76.056 262 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.22 % Allowed : 25.61 % Favored : 73.17 % 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: -2.38 (0.58), residues: 197 helix: -1.34 (0.56), residues: 86 sheet: None (None), residues: 0 loop : -1.79 (0.58), residues: 111 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 8 time to evaluate : 0.187 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 10 average time/residue: 0.1507 time to fit residues: 1.9383 Evaluate side-chains 8 residues out of total 165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 7 time to evaluate : 0.203 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0293 time to fit residues: 0.2829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 0 optimal weight: 50.0000 chunk 13 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 6 optimal weight: 40.0000 chunk 3 optimal weight: 6.9990 chunk 10 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1646 Z= 0.191 Angle : 0.533 4.639 2268 Z= 0.274 Chirality : 0.041 0.142 270 Planarity : 0.005 0.061 284 Dihedral : 9.741 74.586 262 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.83 % Allowed : 28.05 % Favored : 70.12 % 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: -1.95 (0.60), residues: 197 helix: -0.97 (0.58), residues: 86 sheet: None (None), residues: 0 loop : -1.56 (0.60), residues: 111 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 9 time to evaluate : 0.185 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 12 average time/residue: 0.1178 time to fit residues: 1.8405 Evaluate side-chains 8 residues out of total 165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 7 time to evaluate : 0.174 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0188 time to fit residues: 0.2540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 1 optimal weight: 40.0000 chunk 6 optimal weight: 50.0000 chunk 9 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1646 Z= 0.156 Angle : 0.514 4.731 2268 Z= 0.265 Chirality : 0.040 0.139 270 Planarity : 0.005 0.058 284 Dihedral : 9.508 72.139 262 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.61 % Allowed : 30.49 % Favored : 68.90 % 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: -1.68 (0.60), residues: 197 helix: -0.71 (0.59), residues: 85 sheet: None (None), residues: 0 loop : -1.43 (0.59), residues: 112 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 7 time to evaluate : 0.131 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 8 average time/residue: 0.0726 time to fit residues: 0.8779 Evaluate side-chains 7 residues out of total 165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 6 time to evaluate : 0.131 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0165 time to fit residues: 0.1987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 10 optimal weight: 30.0000 chunk 15 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 8 optimal weight: 50.0000 chunk 7 optimal weight: 40.0000 chunk 5 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 1 optimal weight: 30.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 1646 Z= 0.185 Angle : 0.512 4.602 2268 Z= 0.266 Chirality : 0.041 0.130 270 Planarity : 0.005 0.055 284 Dihedral : 9.478 71.412 262 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 31.71 % Favored : 68.29 % 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: -1.46 (0.61), residues: 197 helix: -0.60 (0.60), residues: 85 sheet: None (None), residues: 0 loop : -1.24 (0.60), residues: 112 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 7 residues out of total 165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.172 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.1034 time to fit residues: 1.0919 Evaluate side-chains 7 residues out of total 165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.189 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 14 optimal weight: 30.0000 chunk 16 optimal weight: 10.0000 chunk 17 optimal weight: 30.0000 chunk 10 optimal weight: 50.0000 chunk 7 optimal weight: 40.0000 chunk 13 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 0.0050 chunk 18 optimal weight: 0.2980 chunk 8 optimal weight: 9.9990 overall best weight: 4.2600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1646 Z= 0.160 Angle : 0.511 4.597 2268 Z= 0.263 Chirality : 0.040 0.126 270 Planarity : 0.004 0.055 284 Dihedral : 9.331 69.825 262 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 31.71 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.63), residues: 197 helix: 0.01 (0.64), residues: 77 sheet: None (None), residues: 0 loop : -0.86 (0.60), residues: 120 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.170 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.1179 time to fit residues: 1.3332 Evaluate side-chains 6 residues out of total 165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 6 time to evaluate : 0.178 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 12 optimal weight: 7.9990 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 30.0000 chunk 15 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 9 optimal weight: 30.0000 chunk 16 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 2 optimal weight: 0.1980 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 1646 Z= 0.154 Angle : 0.525 5.976 2268 Z= 0.266 Chirality : 0.040 0.116 270 Planarity : 0.004 0.052 284 Dihedral : 9.176 67.620 262 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 33.54 % Favored : 66.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.63), residues: 197 helix: 0.31 (0.64), residues: 77 sheet: None (None), residues: 0 loop : -0.69 (0.60), residues: 120 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 7 residues out of total 165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.222 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.1002 time to fit residues: 1.1191 Evaluate side-chains 6 residues out of total 165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 6 time to evaluate : 0.189 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 4 optimal weight: 40.0000 chunk 15 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 2 optimal weight: 0.0070 chunk 13 optimal weight: 6.9990 chunk 0 optimal weight: 50.0000 chunk 10 optimal weight: 10.0000 chunk 17 optimal weight: 30.0000 chunk 12 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 overall best weight: 5.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 1646 Z= 0.185 Angle : 0.523 4.773 2268 Z= 0.268 Chirality : 0.040 0.119 270 Planarity : 0.004 0.049 284 Dihedral : 9.251 68.210 262 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.61 % Allowed : 33.54 % Favored : 65.85 % 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: -0.23 (0.64), residues: 197 helix: 0.53 (0.66), residues: 77 sheet: None (None), residues: 0 loop : -0.58 (0.60), residues: 120 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 7 residues out of total 165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 6 time to evaluate : 0.180 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 7 average time/residue: 0.0930 time to fit residues: 1.0327 Evaluate side-chains 6 residues out of total 165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 6 time to evaluate : 0.183 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 10 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 0 optimal weight: 50.0000 chunk 3 optimal weight: 20.0000 chunk 2 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 1 optimal weight: 0.3980 overall best weight: 5.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1646 Z= 0.188 Angle : 0.529 4.637 2268 Z= 0.274 Chirality : 0.041 0.132 270 Planarity : 0.004 0.049 284 Dihedral : 9.276 68.612 262 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.00 % Allowed : 34.15 % Favored : 65.85 % 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: -0.39 (0.63), residues: 197 helix: 0.18 (0.62), residues: 83 sheet: None (None), residues: 0 loop : -0.54 (0.62), residues: 114 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 394 Ramachandran restraints generated. 197 Oldfield, 0 Emsley, 197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 6 residues out of total 165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 6 time to evaluate : 0.181 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.1033 time to fit residues: 0.9787 Evaluate side-chains 6 residues out of total 165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 6 time to evaluate : 0.179 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 4 optimal weight: 30.0000 chunk 12 optimal weight: 0.7980 chunk 6 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 1 optimal weight: 7.9990 chunk 18 optimal weight: 0.1980 chunk 13 optimal weight: 10.0000 chunk 15 optimal weight: 30.0000 chunk 17 optimal weight: 7.9990 overall best weight: 4.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** 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 = 0.3359 r_free = 0.3359 target = 0.044507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.038611 restraints weight = 15733.116| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 3.67 r_work: 0.3041 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1646 Z= 0.184 Angle : 0.529 4.725 2268 Z= 0.273 Chirality : 0.040 0.118 270 Planarity : 0.004 0.048 284 Dihedral : 9.273 68.670 262 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.00 % Allowed : 34.15 % Favored : 65.85 % 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: -0.32 (0.64), residues: 197 helix: 0.20 (0.61), residues: 83 sheet: None (None), residues: 0 loop : -0.45 (0.63), residues: 114 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 730.67 seconds wall clock time: 17 minutes 26.81 seconds (1046.81 seconds total)