Starting phenix.real_space_refine on Wed Nov 13 22:56:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jga_36228/11_2024/8jga_36228.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jga_36228/11_2024/8jga_36228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jga_36228/11_2024/8jga_36228.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jga_36228/11_2024/8jga_36228.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jga_36228/11_2024/8jga_36228.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jga_36228/11_2024/8jga_36228.cif" } resolution = 3.68 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= 0.022 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 7 5.16 5 C 987 2.51 5 N 249 2.21 5 O 273 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 1516 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1516 Classifications: {'peptide': 202} Incomplete info: {'backbone_only': 2} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 191} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.78, per 1000 atoms: 3.15 Number of scatterers: 1516 At special positions: 0 Unit cell: (54.78, 50.63, 55.61, 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 7 16.00 O 273 8.00 N 249 7.00 C 987 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 165 " - pdb=" SG CYS A 203 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 0.39 Conformation dependent library (CDL) restraints added in 215.6 milliseconds 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 362 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 3 sheets defined 58.4% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 20 through 35 removed outlier: 3.506A pdb=" N LEU A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A 31 " --> pdb=" O LYS A 27 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 56 through 62 removed outlier: 4.314A pdb=" N GLU A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N MET A 61 " --> pdb=" O PHE A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 82 Processing helix chain 'A' and resid 93 through 104 Processing helix chain 'A' and resid 113 through 124 removed outlier: 4.002A pdb=" N LYS A 119 " --> pdb=" O THR A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 137 through 145 removed outlier: 4.100A pdb=" N VAL A 141 " --> pdb=" O GLY A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 169 Processing helix chain 'A' and resid 185 through 202 removed outlier: 3.799A pdb=" N ALA A 190 " --> pdb=" O PRO A 186 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU A 191 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU A 198 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS A 199 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 200 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG A 201 " --> pdb=" O VAL A 197 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 15 removed outlier: 6.254A pdb=" N ALA A 14 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N THR A 42 " --> pdb=" O ALA A 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 88 removed outlier: 3.553A pdb=" N MET A 108 " --> pdb=" O ILE A 87 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 127 through 129 removed outlier: 6.784A pdb=" N LEU A 128 " --> pdb=" O VAL A 154 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 65 hydrogen bonds defined for protein. 195 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: 0.45 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: 381 1.33 - 1.46: 306 1.46 - 1.58: 846 1.58 - 1.71: 0 1.71 - 1.83: 12 Bond restraints: 1545 Sorted by residual: bond pdb=" C LYS A 183 " pdb=" O LYS A 183 " ideal model delta sigma weight residual 1.234 1.207 0.026 1.19e-02 7.06e+03 4.92e+00 bond pdb=" C LEU A 181 " pdb=" O LEU A 181 " ideal model delta sigma weight residual 1.235 1.213 0.022 1.26e-02 6.30e+03 3.15e+00 bond pdb=" C VAL A 182 " pdb=" O VAL A 182 " ideal model delta sigma weight residual 1.236 1.218 0.018 1.19e-02 7.06e+03 2.36e+00 bond pdb=" CA LYS A 183 " pdb=" C LYS A 183 " ideal model delta sigma weight residual 1.525 1.506 0.020 1.29e-02 6.01e+03 2.31e+00 bond pdb=" CG LEU A 173 " pdb=" CD1 LEU A 173 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.61e+00 ... (remaining 1540 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 1985 1.63 - 3.27: 76 3.27 - 4.90: 19 4.90 - 6.54: 2 6.54 - 8.17: 2 Bond angle restraints: 2084 Sorted by residual: angle pdb=" C LYS A 183 " pdb=" N GLY A 184 " pdb=" CA GLY A 184 " ideal model delta sigma weight residual 121.23 125.06 -3.83 1.34e+00 5.57e-01 8.16e+00 angle pdb=" N ALA A 180 " pdb=" CA ALA A 180 " pdb=" C ALA A 180 " ideal model delta sigma weight residual 112.59 109.52 3.07 1.22e+00 6.72e-01 6.33e+00 angle pdb=" C ASN A 19 " pdb=" N SER A 20 " pdb=" CA SER A 20 " ideal model delta sigma weight residual 121.54 126.00 -4.46 1.91e+00 2.74e-01 5.46e+00 angle pdb=" CA LEU A 55 " pdb=" CB LEU A 55 " pdb=" CG LEU A 55 " ideal model delta sigma weight residual 116.30 124.47 -8.17 3.50e+00 8.16e-02 5.45e+00 angle pdb=" C VAL A 164 " pdb=" N CYS A 165 " pdb=" CA CYS A 165 " ideal model delta sigma weight residual 121.58 117.20 4.38 1.95e+00 2.63e-01 5.04e+00 ... (remaining 2079 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 15.82: 821 15.82 - 31.64: 81 31.64 - 47.46: 22 47.46 - 63.28: 7 63.28 - 79.10: 1 Dihedral angle restraints: 932 sinusoidal: 368 harmonic: 564 Sorted by residual: dihedral pdb=" CB CYS A 165 " pdb=" SG CYS A 165 " pdb=" SG CYS A 203 " pdb=" CB CYS A 203 " ideal model delta sinusoidal sigma weight residual 93.00 42.70 50.30 1 1.00e+01 1.00e-02 3.47e+01 dihedral pdb=" CA LYS A 152 " pdb=" C LYS A 152 " pdb=" N PHE A 153 " pdb=" CA PHE A 153 " ideal model delta harmonic sigma weight residual -180.00 -162.76 -17.24 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA GLY A 202 " pdb=" C GLY A 202 " pdb=" N CYS A 203 " pdb=" CA CYS A 203 " ideal model delta harmonic sigma weight residual -180.00 -162.98 -17.02 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 139 0.039 - 0.079: 66 0.079 - 0.118: 30 0.118 - 0.157: 8 0.157 - 0.197: 1 Chirality restraints: 244 Sorted by residual: chirality pdb=" CG LEU A 181 " pdb=" CB LEU A 181 " pdb=" CD1 LEU A 181 " pdb=" CD2 LEU A 181 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.66e-01 chirality pdb=" CA PRO A 186 " pdb=" N PRO A 186 " pdb=" C PRO A 186 " pdb=" CB PRO A 186 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.66e-01 chirality pdb=" CA ILE A 64 " pdb=" N ILE A 64 " pdb=" C ILE A 64 " pdb=" CB ILE A 64 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.47e-01 ... (remaining 241 not shown) Planarity restraints: 263 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 185 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO A 186 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 186 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 186 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 108 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.13e+00 pdb=" N PRO A 109 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 109 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 109 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 183 " 0.007 2.00e-02 2.50e+03 1.40e-02 1.95e+00 pdb=" C LYS A 183 " -0.024 2.00e-02 2.50e+03 pdb=" O LYS A 183 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY A 184 " 0.008 2.00e-02 2.50e+03 ... (remaining 260 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 254 2.76 - 3.30: 1514 3.30 - 3.83: 2527 3.83 - 4.37: 2950 4.37 - 4.90: 5061 Nonbonded interactions: 12306 Sorted by model distance: nonbonded pdb=" O ASP A 49 " pdb=" OG SER A 82 " model vdw 2.230 3.040 nonbonded pdb=" OG SER A 89 " pdb=" OH TYR A 107 " model vdw 2.252 3.040 nonbonded pdb=" OG1 THR A 126 " pdb=" O ASN A 150 " model vdw 2.257 3.040 nonbonded pdb=" OG SER A 97 " pdb=" NE2 HIS A 125 " model vdw 2.266 3.120 nonbonded pdb=" NZ LYS A 27 " pdb=" O GLY A 184 " model vdw 2.383 3.120 ... (remaining 12301 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 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: 5.490 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 12.320 Find NCS groups from input model: 0.020 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 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 : 0.005 0.042 1545 Z= 0.320 Angle : 0.811 8.171 2084 Z= 0.452 Chirality : 0.054 0.197 244 Planarity : 0.006 0.045 263 Dihedral : 14.340 79.102 567 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.00 % Favored : 92.50 % Rotamer: Outliers : 1.24 % Allowed : 0.62 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.18 (0.60), residues: 200 helix: -1.12 (0.51), residues: 108 sheet: -1.53 (0.88), residues: 30 loop : -1.61 (0.84), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 167 HIS 0.002 0.001 HIS A 91 PHE 0.017 0.002 PHE A 99 TYR 0.005 0.001 TYR A 107 ARG 0.009 0.002 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.189 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 28 average time/residue: 0.2003 time to fit residues: 6.2976 Evaluate side-chains 21 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 1545 Z= 0.206 Angle : 0.695 9.635 2084 Z= 0.339 Chirality : 0.048 0.132 244 Planarity : 0.005 0.046 263 Dihedral : 5.781 26.949 209 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.11 % Allowed : 11.18 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.96 (0.61), residues: 200 helix: -0.99 (0.51), residues: 108 sheet: -1.24 (0.95), residues: 30 loop : -1.53 (0.83), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 167 HIS 0.001 0.001 HIS A 91 PHE 0.009 0.001 PHE A 168 TYR 0.005 0.001 TYR A 107 ARG 0.002 0.000 ARG A 17 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.178 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 23 average time/residue: 0.1810 time to fit residues: 4.7476 Evaluate side-chains 23 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 183 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 0.0770 chunk 9 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 1545 Z= 0.207 Angle : 0.648 9.014 2084 Z= 0.318 Chirality : 0.048 0.134 244 Planarity : 0.005 0.044 263 Dihedral : 5.572 29.514 209 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.73 % Allowed : 14.29 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.71 (0.61), residues: 200 helix: -0.76 (0.51), residues: 109 sheet: -1.29 (0.95), residues: 30 loop : -1.36 (0.86), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 167 HIS 0.001 0.001 HIS A 91 PHE 0.019 0.002 PHE A 32 TYR 0.004 0.001 TYR A 107 ARG 0.002 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.190 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 22 average time/residue: 0.1846 time to fit residues: 4.6349 Evaluate side-chains 23 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 183 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 9 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1545 Z= 0.198 Angle : 0.611 7.989 2084 Z= 0.303 Chirality : 0.047 0.135 244 Planarity : 0.005 0.042 263 Dihedral : 5.308 29.488 209 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.73 % Allowed : 17.39 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.57 (0.62), residues: 200 helix: -0.58 (0.52), residues: 109 sheet: -1.28 (0.94), residues: 30 loop : -1.43 (0.84), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 167 HIS 0.001 0.001 HIS A 91 PHE 0.016 0.002 PHE A 32 TYR 0.003 0.001 TYR A 107 ARG 0.002 0.001 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.183 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 25 average time/residue: 0.1302 time to fit residues: 3.8843 Evaluate side-chains 23 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 183 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 4 optimal weight: 0.0070 chunk 19 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1545 Z= 0.179 Angle : 0.613 7.024 2084 Z= 0.303 Chirality : 0.046 0.133 244 Planarity : 0.004 0.040 263 Dihedral : 5.117 28.549 209 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.11 % Allowed : 18.63 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.63), residues: 200 helix: -0.44 (0.53), residues: 109 sheet: -1.05 (0.92), residues: 32 loop : -1.27 (0.88), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 167 HIS 0.001 0.000 HIS A 91 PHE 0.012 0.001 PHE A 32 TYR 0.003 0.001 TYR A 107 ARG 0.002 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.180 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 22 average time/residue: 0.1427 time to fit residues: 3.7080 Evaluate side-chains 23 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 115 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1545 Z= 0.181 Angle : 0.590 6.822 2084 Z= 0.292 Chirality : 0.046 0.134 244 Planarity : 0.004 0.039 263 Dihedral : 4.566 13.747 205 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.48 % Allowed : 21.74 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.30 (0.62), residues: 200 helix: -0.44 (0.53), residues: 109 sheet: -1.13 (0.90), residues: 32 loop : -1.16 (0.87), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 167 HIS 0.001 0.000 HIS A 91 PHE 0.010 0.001 PHE A 32 TYR 0.003 0.001 TYR A 107 ARG 0.002 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.180 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 23 average time/residue: 0.1120 time to fit residues: 3.1458 Evaluate side-chains 21 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 115 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1545 Z= 0.175 Angle : 0.573 6.024 2084 Z= 0.284 Chirality : 0.046 0.133 244 Planarity : 0.004 0.038 263 Dihedral : 4.525 13.903 205 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.86 % Allowed : 22.36 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.19 (0.62), residues: 200 helix: -0.32 (0.53), residues: 109 sheet: -1.06 (0.88), residues: 32 loop : -1.18 (0.86), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 167 HIS 0.001 0.000 HIS A 10 PHE 0.010 0.001 PHE A 32 TYR 0.003 0.001 TYR A 107 ARG 0.002 0.001 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.196 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 20 average time/residue: 0.1276 time to fit residues: 3.1165 Evaluate side-chains 20 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 115 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 9 optimal weight: 0.2980 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 1545 Z= 0.156 Angle : 0.552 5.342 2084 Z= 0.275 Chirality : 0.046 0.132 244 Planarity : 0.004 0.037 263 Dihedral : 4.409 13.353 205 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.48 % Allowed : 22.36 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.08 (0.62), residues: 200 helix: -0.21 (0.53), residues: 109 sheet: -1.09 (0.87), residues: 32 loop : -1.13 (0.87), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 167 HIS 0.001 0.000 HIS A 91 PHE 0.010 0.001 PHE A 32 TYR 0.001 0.001 TYR A 107 ARG 0.001 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.170 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 23 average time/residue: 0.1187 time to fit residues: 3.4254 Evaluate side-chains 22 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 181 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 13 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1545 Z= 0.175 Angle : 0.662 14.858 2084 Z= 0.298 Chirality : 0.046 0.133 244 Planarity : 0.004 0.036 263 Dihedral : 4.434 13.492 205 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.48 % Allowed : 22.36 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.62), residues: 200 helix: -0.23 (0.52), residues: 109 sheet: -1.14 (0.86), residues: 32 loop : -1.11 (0.87), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP A 167 HIS 0.001 0.000 HIS A 91 PHE 0.009 0.001 PHE A 32 TYR 0.002 0.001 TYR A 107 ARG 0.002 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.182 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 22 average time/residue: 0.1031 time to fit residues: 2.7844 Evaluate side-chains 23 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 181 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 18 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1545 Z= 0.212 Angle : 0.653 12.392 2084 Z= 0.304 Chirality : 0.047 0.137 244 Planarity : 0.004 0.036 263 Dihedral : 4.545 13.867 205 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.86 % Allowed : 23.60 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.61), residues: 200 helix: -0.31 (0.52), residues: 109 sheet: -1.05 (0.87), residues: 32 loop : -1.05 (0.88), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 167 HIS 0.001 0.001 HIS A 91 PHE 0.009 0.001 PHE A 86 TYR 0.003 0.001 TYR A 107 ARG 0.003 0.001 ARG A 77 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.173 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 21 average time/residue: 0.1307 time to fit residues: 3.3641 Evaluate side-chains 22 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 181 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 8 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.124345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.109207 restraints weight = 2041.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.112155 restraints weight = 1217.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.114238 restraints weight = 840.828| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1545 Z= 0.175 Angle : 0.629 12.482 2084 Z= 0.292 Chirality : 0.046 0.133 244 Planarity : 0.004 0.036 263 Dihedral : 4.475 13.461 205 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.86 % Allowed : 24.22 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.06 (0.61), residues: 200 helix: -0.25 (0.52), residues: 109 sheet: -1.00 (0.88), residues: 32 loop : -1.03 (0.87), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 167 HIS 0.001 0.000 HIS A 91 PHE 0.009 0.001 PHE A 32 TYR 0.002 0.001 TYR A 107 ARG 0.001 0.000 ARG A 17 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1155.50 seconds wall clock time: 23 minutes 4.73 seconds (1384.73 seconds total)