Starting phenix.real_space_refine on Mon Sep 23 12:16:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve7_43167/09_2024/8ve7_43167.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve7_43167/09_2024/8ve7_43167.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve7_43167/09_2024/8ve7_43167.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve7_43167/09_2024/8ve7_43167.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve7_43167/09_2024/8ve7_43167.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve7_43167/09_2024/8ve7_43167.cif" } resolution = 4.0 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= -0.000 sd= 0.002 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 6 5.16 5 C 1434 2.51 5 N 387 2.21 5 O 437 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 2264 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2264 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 6, 'TRANS': 287} Time building chain proxies: 2.23, per 1000 atoms: 0.98 Number of scatterers: 2264 At special positions: 0 Unit cell: (53.71, 57.64, 115.28, 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 6 16.00 O 437 8.00 N 387 7.00 C 1434 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 - 3.00 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: 0.65 Conformation dependent library (CDL) restraints added in 306.5 milliseconds 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 538 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 75.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 24 through 45 Processing helix chain 'A' and resid 49 through 72 Processing helix chain 'A' and resid 80 through 97 removed outlier: 3.887A pdb=" N ILE A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N MET A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 137 Processing helix chain 'A' and resid 139 through 175 Processing helix chain 'A' and resid 176 through 186 removed outlier: 4.533A pdb=" N VAL A 180 " --> pdb=" O GLN A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 208 Processing helix chain 'A' and resid 209 through 219 removed outlier: 3.672A pdb=" N VAL A 213 " --> pdb=" O HIS A 209 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N HIS A 219 " --> pdb=" O VAL A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 240 Processing helix chain 'A' and resid 242 through 252 Processing helix chain 'A' and resid 265 through 273 removed outlier: 3.654A pdb=" N LEU A 269 " --> pdb=" O THR A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 285 Processing helix chain 'A' and resid 298 through 307 removed outlier: 3.532A pdb=" N GLY A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 316 removed outlier: 3.930A pdb=" N ALA A 312 " --> pdb=" O ASN A 308 " (cutoff:3.500A) 157 hydrogen bonds defined for protein. 471 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: 0.58 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 776 1.34 - 1.46: 222 1.46 - 1.57: 1288 1.57 - 1.69: 0 1.69 - 1.80: 11 Bond restraints: 2297 Sorted by residual: bond pdb=" CG GLU A 214 " pdb=" CD GLU A 214 " ideal model delta sigma weight residual 1.516 1.493 0.023 2.50e-02 1.60e+03 8.43e-01 bond pdb=" CD GLU A 214 " pdb=" OE1 GLU A 214 " ideal model delta sigma weight residual 1.249 1.233 0.016 1.90e-02 2.77e+03 7.19e-01 bond pdb=" CB GLN A 60 " pdb=" CG GLN A 60 " ideal model delta sigma weight residual 1.520 1.499 0.021 3.00e-02 1.11e+03 4.72e-01 bond pdb=" CA GLN A 60 " pdb=" C GLN A 60 " ideal model delta sigma weight residual 1.523 1.515 0.009 1.30e-02 5.92e+03 4.55e-01 bond pdb=" CB ARG A 123 " pdb=" CG ARG A 123 " ideal model delta sigma weight residual 1.520 1.501 0.019 3.00e-02 1.11e+03 4.04e-01 ... (remaining 2292 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.98: 2867 0.98 - 1.95: 191 1.95 - 2.93: 30 2.93 - 3.90: 10 3.90 - 4.88: 10 Bond angle restraints: 3108 Sorted by residual: angle pdb=" C GLN A 176 " pdb=" CA GLN A 176 " pdb=" CB GLN A 176 " ideal model delta sigma weight residual 110.19 115.07 -4.88 1.62e+00 3.81e-01 9.07e+00 angle pdb=" C ASN A 308 " pdb=" CA ASN A 308 " pdb=" CB ASN A 308 " ideal model delta sigma weight residual 110.22 114.17 -3.95 1.67e+00 3.59e-01 5.59e+00 angle pdb=" N GLU A 214 " pdb=" CA GLU A 214 " pdb=" CB GLU A 214 " ideal model delta sigma weight residual 110.01 113.37 -3.36 1.45e+00 4.76e-01 5.37e+00 angle pdb=" CA GLN A 176 " pdb=" CB GLN A 176 " pdb=" CG GLN A 176 " ideal model delta sigma weight residual 114.10 118.14 -4.04 2.00e+00 2.50e-01 4.09e+00 angle pdb=" CA GLN A 196 " pdb=" CB GLN A 196 " pdb=" CG GLN A 196 " ideal model delta sigma weight residual 114.10 117.84 -3.74 2.00e+00 2.50e-01 3.50e+00 ... (remaining 3103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 1303 17.80 - 35.59: 73 35.59 - 53.38: 4 53.38 - 71.18: 2 71.18 - 88.97: 2 Dihedral angle restraints: 1384 sinusoidal: 547 harmonic: 837 Sorted by residual: dihedral pdb=" CA GLN A 176 " pdb=" C GLN A 176 " pdb=" N ASP A 177 " pdb=" CA ASP A 177 " ideal model delta harmonic sigma weight residual -180.00 -146.04 -33.96 0 5.00e+00 4.00e-02 4.61e+01 dihedral pdb=" CB GLU A 163 " pdb=" CG GLU A 163 " pdb=" CD GLU A 163 " pdb=" OE1 GLU A 163 " ideal model delta sinusoidal sigma weight residual 0.00 -81.63 81.63 1 3.00e+01 1.11e-03 9.11e+00 dihedral pdb=" CG LYS A 53 " pdb=" CD LYS A 53 " pdb=" CE LYS A 53 " pdb=" NZ LYS A 53 " ideal model delta sinusoidal sigma weight residual 60.00 105.56 -45.56 3 1.50e+01 4.44e-03 8.19e+00 ... (remaining 1381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 194 0.022 - 0.044: 82 0.044 - 0.066: 52 0.066 - 0.087: 30 0.087 - 0.109: 5 Chirality restraints: 363 Sorted by residual: chirality pdb=" CA ILE A 76 " pdb=" N ILE A 76 " pdb=" C ILE A 76 " pdb=" CB ILE A 76 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 2.98e-01 chirality pdb=" CA VAL A 98 " pdb=" N VAL A 98 " pdb=" C VAL A 98 " pdb=" CB VAL A 98 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.86e-01 chirality pdb=" CG LEU A 234 " pdb=" CB LEU A 234 " pdb=" CD1 LEU A 234 " pdb=" CD2 LEU A 234 " both_signs ideal model delta sigma weight residual False -2.59 -2.49 -0.10 2.00e-01 2.50e+01 2.65e-01 ... (remaining 360 not shown) Planarity restraints: 403 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 206 " -0.005 2.00e-02 2.50e+03 6.60e-03 1.09e+00 pdb=" CG TRP A 206 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP A 206 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP A 206 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 206 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 206 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 206 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 206 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 206 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 206 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 308 " 0.005 2.00e-02 2.50e+03 9.04e-03 8.17e-01 pdb=" C ASN A 308 " -0.016 2.00e-02 2.50e+03 pdb=" O ASN A 308 " 0.006 2.00e-02 2.50e+03 pdb=" N GLU A 309 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 38 " 0.004 2.00e-02 2.50e+03 8.16e-03 6.65e-01 pdb=" C THR A 38 " -0.014 2.00e-02 2.50e+03 pdb=" O THR A 38 " 0.005 2.00e-02 2.50e+03 pdb=" N SER A 39 " 0.005 2.00e-02 2.50e+03 ... (remaining 400 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 53 2.69 - 3.24: 2431 3.24 - 3.80: 3727 3.80 - 4.35: 4670 4.35 - 4.90: 7332 Nonbonded interactions: 18213 Sorted by model distance: nonbonded pdb=" OG1 THR A 38 " pdb=" OE1 GLN A 60 " model vdw 2.139 3.040 nonbonded pdb=" OG1 THR A 232 " pdb=" ND1 HIS A 235 " model vdw 2.141 3.120 nonbonded pdb=" O GLN A 196 " pdb=" OG1 THR A 228 " model vdw 2.291 3.040 nonbonded pdb=" O PRO A 210 " pdb=" N VAL A 213 " model vdw 2.327 3.120 nonbonded pdb=" O ASP A 239 " pdb=" NH1 ARG A 273 " model vdw 2.345 3.120 ... (remaining 18208 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: 0.600 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 11.050 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 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 : 0.003 0.023 2297 Z= 0.216 Angle : 0.606 4.878 3108 Z= 0.345 Chirality : 0.037 0.109 363 Planarity : 0.003 0.020 403 Dihedral : 11.541 88.973 846 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: 2.80 (0.49), residues: 292 helix: 2.03 (0.34), residues: 217 sheet: None (None), residues: 0 loop : 1.61 (0.76), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 206 HIS 0.006 0.001 HIS A 268 PHE 0.004 0.001 PHE A 154 TYR 0.009 0.001 TYR A 64 ARG 0.003 0.000 ARG A 226 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 193 HIS cc_start: 0.8980 (p90) cc_final: 0.8692 (p90) REVERT: A 257 ASN cc_start: 0.7832 (m-40) cc_final: 0.7593 (m110) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1641 time to fit residues: 11.5481 Evaluate side-chains 35 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 24 optimal weight: 6.9990 chunk 21 optimal weight: 20.0000 chunk 12 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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: 0.8026 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2297 Z= 0.196 Angle : 0.553 5.876 3108 Z= 0.290 Chirality : 0.038 0.117 363 Planarity : 0.003 0.020 403 Dihedral : 4.009 24.616 311 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.97 % Allowed : 7.20 % Favored : 89.83 % 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: 3.11 (0.47), residues: 292 helix: 2.45 (0.33), residues: 216 sheet: None (None), residues: 0 loop : 1.03 (0.72), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 86 HIS 0.005 0.001 HIS A 209 PHE 0.018 0.001 PHE A 103 TYR 0.005 0.001 TYR A 252 ARG 0.002 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 36 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 235 HIS cc_start: 0.7038 (m170) cc_final: 0.6742 (m90) REVERT: A 257 ASN cc_start: 0.7882 (m-40) cc_final: 0.7594 (m110) outliers start: 7 outliers final: 3 residues processed: 41 average time/residue: 0.1365 time to fit residues: 7.0315 Evaluate side-chains 36 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 133 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 14 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 26 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 19 optimal weight: 0.4980 chunk 13 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2297 Z= 0.232 Angle : 0.551 5.987 3108 Z= 0.292 Chirality : 0.038 0.113 363 Planarity : 0.003 0.023 403 Dihedral : 3.935 25.377 311 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.54 % Allowed : 11.02 % Favored : 86.44 % 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: 3.10 (0.47), residues: 292 helix: 2.48 (0.33), residues: 216 sheet: None (None), residues: 0 loop : 0.91 (0.71), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 206 HIS 0.003 0.001 HIS A 202 PHE 0.015 0.001 PHE A 103 TYR 0.006 0.001 TYR A 94 ARG 0.002 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 181 ARG cc_start: 0.8550 (ptp90) cc_final: 0.8301 (ptp90) REVERT: A 257 ASN cc_start: 0.7873 (m-40) cc_final: 0.7613 (m110) outliers start: 6 outliers final: 3 residues processed: 37 average time/residue: 0.1159 time to fit residues: 5.4134 Evaluate side-chains 33 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 30 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 133 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 12 optimal weight: 0.4980 chunk 17 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2297 Z= 0.243 Angle : 0.547 5.886 3108 Z= 0.288 Chirality : 0.039 0.116 363 Planarity : 0.003 0.024 403 Dihedral : 4.030 25.704 311 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.39 % Allowed : 12.29 % Favored : 84.32 % 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: 3.16 (0.48), residues: 292 helix: 2.52 (0.34), residues: 216 sheet: None (None), residues: 0 loop : 0.91 (0.71), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 206 HIS 0.008 0.002 HIS A 193 PHE 0.013 0.001 PHE A 103 TYR 0.007 0.001 TYR A 94 ARG 0.002 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 33 time to evaluate : 0.274 Fit side-chains REVERT: A 181 ARG cc_start: 0.8544 (ptp90) cc_final: 0.8298 (ptp90) REVERT: A 234 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7430 (pp) REVERT: A 257 ASN cc_start: 0.8083 (m-40) cc_final: 0.7757 (m110) outliers start: 8 outliers final: 5 residues processed: 39 average time/residue: 0.1304 time to fit residues: 6.2846 Evaluate side-chains 36 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 30 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 234 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 11 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 7 optimal weight: 0.0870 chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2297 Z= 0.196 Angle : 0.538 5.858 3108 Z= 0.287 Chirality : 0.038 0.110 363 Planarity : 0.003 0.026 403 Dihedral : 4.054 25.926 311 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.39 % Allowed : 13.56 % Favored : 83.05 % 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: 3.21 (0.48), residues: 292 helix: 2.60 (0.34), residues: 216 sheet: None (None), residues: 0 loop : 0.80 (0.71), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 206 HIS 0.009 0.002 HIS A 193 PHE 0.012 0.001 PHE A 103 TYR 0.006 0.001 TYR A 252 ARG 0.002 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 32 time to evaluate : 0.264 Fit side-chains REVERT: A 181 ARG cc_start: 0.8519 (ptp90) cc_final: 0.8277 (ptp90) REVERT: A 257 ASN cc_start: 0.7867 (m-40) cc_final: 0.7610 (m110) outliers start: 8 outliers final: 6 residues processed: 38 average time/residue: 0.1140 time to fit residues: 5.4466 Evaluate side-chains 36 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 30 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 214 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 28 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 12 optimal weight: 0.6980 chunk 2 optimal weight: 0.0770 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 0.4980 chunk 3 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 20.0000 chunk 17 optimal weight: 0.1980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2297 Z= 0.144 Angle : 0.493 6.100 3108 Z= 0.264 Chirality : 0.037 0.113 363 Planarity : 0.003 0.030 403 Dihedral : 4.014 26.442 311 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.12 % Allowed : 16.95 % Favored : 80.93 % 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: 3.13 (0.48), residues: 292 helix: 2.55 (0.35), residues: 216 sheet: None (None), residues: 0 loop : 0.73 (0.70), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 206 HIS 0.009 0.001 HIS A 193 PHE 0.010 0.001 PHE A 103 TYR 0.007 0.001 TYR A 64 ARG 0.001 0.000 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 37 time to evaluate : 0.271 Fit side-chains REVERT: A 181 ARG cc_start: 0.8458 (ptp90) cc_final: 0.8220 (ptp90) REVERT: A 257 ASN cc_start: 0.7814 (m-40) cc_final: 0.7539 (m110) REVERT: A 281 VAL cc_start: 0.9232 (t) cc_final: 0.8985 (p) outliers start: 5 outliers final: 2 residues processed: 41 average time/residue: 0.1115 time to fit residues: 5.7769 Evaluate side-chains 38 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 214 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 17 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 5 optimal weight: 0.0270 chunk 19 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2297 Z= 0.142 Angle : 0.499 5.779 3108 Z= 0.261 Chirality : 0.037 0.113 363 Planarity : 0.003 0.031 403 Dihedral : 3.907 25.638 311 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.69 % Allowed : 18.22 % Favored : 80.08 % 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: 3.12 (0.48), residues: 292 helix: 2.61 (0.34), residues: 215 sheet: None (None), residues: 0 loop : 0.54 (0.69), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 206 HIS 0.011 0.001 HIS A 193 PHE 0.010 0.001 PHE A 103 TYR 0.005 0.001 TYR A 145 ARG 0.001 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 0.278 Fit side-chains REVERT: A 77 GLU cc_start: 0.8683 (tp30) cc_final: 0.8187 (tm-30) REVERT: A 257 ASN cc_start: 0.7759 (m-40) cc_final: 0.7457 (m110) REVERT: A 281 VAL cc_start: 0.9262 (t) cc_final: 0.9016 (p) outliers start: 4 outliers final: 3 residues processed: 40 average time/residue: 0.1413 time to fit residues: 6.9064 Evaluate side-chains 38 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 214 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 26 optimal weight: 20.0000 chunk 24 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 17 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2297 Z= 0.214 Angle : 0.574 6.311 3108 Z= 0.298 Chirality : 0.038 0.112 363 Planarity : 0.003 0.030 403 Dihedral : 3.915 25.492 311 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.81 % Allowed : 17.37 % Favored : 78.81 % 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: 3.03 (0.48), residues: 292 helix: 2.58 (0.34), residues: 216 sheet: None (None), residues: 0 loop : 0.35 (0.68), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 206 HIS 0.012 0.002 HIS A 193 PHE 0.011 0.001 PHE A 103 TYR 0.007 0.001 TYR A 145 ARG 0.001 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 33 time to evaluate : 0.268 Fit side-chains REVERT: A 181 ARG cc_start: 0.8532 (ptp90) cc_final: 0.8285 (ptp90) REVERT: A 257 ASN cc_start: 0.7758 (m-40) cc_final: 0.7484 (m110) outliers start: 9 outliers final: 6 residues processed: 40 average time/residue: 0.1085 time to fit residues: 5.4755 Evaluate side-chains 37 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 31 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 269 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 2 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2297 Z= 0.217 Angle : 0.587 6.140 3108 Z= 0.305 Chirality : 0.039 0.109 363 Planarity : 0.003 0.030 403 Dihedral : 3.948 25.094 311 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.81 % Allowed : 17.80 % Favored : 78.39 % 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: 2.95 (0.48), residues: 292 helix: 2.57 (0.34), residues: 215 sheet: None (None), residues: 0 loop : 0.17 (0.68), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 206 HIS 0.012 0.002 HIS A 193 PHE 0.010 0.001 PHE A 103 TYR 0.006 0.001 TYR A 94 ARG 0.001 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 34 time to evaluate : 0.253 Fit side-chains REVERT: A 181 ARG cc_start: 0.8527 (ptp90) cc_final: 0.8286 (ptp90) REVERT: A 257 ASN cc_start: 0.7785 (m-40) cc_final: 0.7532 (m110) outliers start: 9 outliers final: 7 residues processed: 40 average time/residue: 0.1112 time to fit residues: 5.5728 Evaluate side-chains 39 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 32 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 269 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 21 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 23 optimal weight: 20.0000 chunk 9 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2297 Z= 0.173 Angle : 0.571 6.902 3108 Z= 0.299 Chirality : 0.039 0.188 363 Planarity : 0.003 0.030 403 Dihedral : 3.955 26.133 311 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.54 % Allowed : 19.49 % Favored : 77.97 % 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: 2.99 (0.48), residues: 292 helix: 2.62 (0.34), residues: 215 sheet: None (None), residues: 0 loop : 0.12 (0.69), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 206 HIS 0.012 0.002 HIS A 193 PHE 0.010 0.001 PHE A 103 TYR 0.007 0.001 TYR A 64 ARG 0.002 0.000 ARG A 273 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 34 time to evaluate : 0.255 Fit side-chains REVERT: A 181 ARG cc_start: 0.8493 (ptp90) cc_final: 0.8263 (ptp90) REVERT: A 257 ASN cc_start: 0.7658 (m-40) cc_final: 0.7423 (m110) outliers start: 6 outliers final: 5 residues processed: 39 average time/residue: 0.1164 time to fit residues: 5.7288 Evaluate side-chains 38 residues out of total 236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 33 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 269 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 28 optimal weight: 8.9990 chunk 1 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 HIS ** 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 = 0.4117 r_free = 0.4117 target = 0.127811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.087027 restraints weight = 6077.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.089097 restraints weight = 3009.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.090254 restraints weight = 1917.740| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2297 Z= 0.193 Angle : 0.593 6.625 3108 Z= 0.307 Chirality : 0.040 0.178 363 Planarity : 0.003 0.030 403 Dihedral : 3.896 25.483 311 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.54 % Allowed : 19.49 % Favored : 77.97 % 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: 2.88 (0.48), residues: 292 helix: 2.51 (0.34), residues: 217 sheet: None (None), residues: 0 loop : 0.12 (0.69), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 206 HIS 0.012 0.002 HIS A 193 PHE 0.010 0.001 PHE A 103 TYR 0.005 0.001 TYR A 94 ARG 0.002 0.000 ARG A 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 894.51 seconds wall clock time: 16 minutes 55.51 seconds (1015.51 seconds total)