Starting phenix.real_space_refine on Mon Jan 13 13:48:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ve7_43167/01_2025/8ve7_43167.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ve7_43167/01_2025/8ve7_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/cci-nas-00/data/ceres_data/8ve7_43167/01_2025/8ve7_43167.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ve7_43167/01_2025/8ve7_43167.map" model { file = "/net/cci-nas-00/data/ceres_data/8ve7_43167/01_2025/8ve7_43167.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ve7_43167/01_2025/8ve7_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-5571/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: 2.33, per 1000 atoms: 1.03 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: 0.58 Conformation dependent library (CDL) restraints added in 297.8 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: 0.60 Time building geometry restraints manager: 0.68 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: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 11.260 Find NCS groups from input model: 0.020 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.060 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.241 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: 0.1717 time to fit residues: 12.0441 Evaluate side-chains 35 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.127427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.087286 restraints weight = 6081.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.089469 restraints weight = 2956.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.090804 restraints weight = 1867.784| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 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 to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 235 HIS cc_start: 0.7099 (m170) cc_final: 0.6820 (m90) REVERT: A 257 ASN cc_start: 0.7937 (m-40) cc_final: 0.7737 (m110) outliers start: 7 outliers final: 3 residues processed: 41 average time/residue: 0.1225 time to fit residues: 6.3527 Evaluate side-chains 36 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 21 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.124790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.082921 restraints weight = 6139.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.085010 restraints weight = 3057.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.086242 restraints weight = 1969.048| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2297 Z= 0.285 Angle : 0.592 5.993 3108 Z= 0.310 Chirality : 0.039 0.115 363 Planarity : 0.003 0.024 403 Dihedral : 3.983 25.080 311 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.97 % Allowed : 10.59 % 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: 2.99 (0.47), residues: 292 helix: 2.40 (0.33), residues: 216 sheet: None (None), residues: 0 loop : 0.89 (0.71), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 86 HIS 0.004 0.001 HIS A 202 PHE 0.016 0.002 PHE A 103 TYR 0.007 0.001 TYR A 94 ARG 0.003 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 41 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.249 Fit side-chains REVERT: A 181 ARG cc_start: 0.8693 (ptp90) cc_final: 0.8461 (ptp90) REVERT: A 235 HIS cc_start: 0.7171 (m170) cc_final: 0.6893 (m90) outliers start: 7 outliers final: 4 residues processed: 39 average time/residue: 0.1143 time to fit residues: 5.5976 Evaluate side-chains 32 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 8 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 0.3980 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4119 r_free = 0.4119 target = 0.127450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.087117 restraints weight = 6106.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.089203 restraints weight = 2975.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.090433 restraints weight = 1874.401| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3117 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= 0.169 Angle : 0.499 5.934 3108 Z= 0.268 Chirality : 0.037 0.114 363 Planarity : 0.003 0.024 403 Dihedral : 4.015 26.229 311 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.69 % Allowed : 14.83 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.16 (0.48), residues: 292 helix: 2.56 (0.34), residues: 216 sheet: None (None), residues: 0 loop : 0.80 (0.70), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 206 HIS 0.006 0.001 HIS A 193 PHE 0.021 0.001 PHE A 103 TYR 0.007 0.001 TYR A 64 ARG 0.001 0.000 ARG A 124 *********************** 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 36 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.253 Fit side-chains REVERT: A 181 ARG cc_start: 0.8609 (ptp90) cc_final: 0.8371 (ptp90) REVERT: A 234 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7690 (pp) REVERT: A 235 HIS cc_start: 0.6751 (m170) cc_final: 0.6530 (m90) outliers start: 4 outliers final: 1 residues processed: 35 average time/residue: 0.1189 time to fit residues: 5.2495 Evaluate side-chains 32 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 14 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.127749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.087597 restraints weight = 6209.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.089723 restraints weight = 3011.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.090902 restraints weight = 1897.411| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2297 Z= 0.155 Angle : 0.484 5.847 3108 Z= 0.259 Chirality : 0.037 0.112 363 Planarity : 0.003 0.025 403 Dihedral : 3.965 26.377 311 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.69 % Allowed : 15.25 % 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: 3.22 (0.48), residues: 292 helix: 2.63 (0.34), residues: 216 sheet: None (None), residues: 0 loop : 0.73 (0.69), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 206 HIS 0.008 0.001 HIS A 193 PHE 0.015 0.001 PHE A 103 TYR 0.005 0.001 TYR A 145 ARG 0.001 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 36 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.265 Fit side-chains REVERT: A 181 ARG cc_start: 0.8616 (ptp90) cc_final: 0.8380 (ptp90) REVERT: A 234 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7779 (pp) outliers start: 4 outliers final: 1 residues processed: 35 average time/residue: 0.1164 time to fit residues: 5.1595 Evaluate side-chains 32 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 234 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 HIS ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.127434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.087337 restraints weight = 6145.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.089492 restraints weight = 2918.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.090771 restraints weight = 1810.898| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2297 Z= 0.168 Angle : 0.531 10.627 3108 Z= 0.271 Chirality : 0.038 0.111 363 Planarity : 0.003 0.024 403 Dihedral : 3.947 25.568 311 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.97 % Allowed : 15.25 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.18 (0.48), residues: 292 helix: 2.62 (0.34), residues: 216 sheet: None (None), residues: 0 loop : 0.65 (0.69), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 206 HIS 0.009 0.002 HIS A 193 PHE 0.005 0.001 PHE A 103 TYR 0.007 0.001 TYR A 64 ARG 0.001 0.000 ARG A 124 *********************** 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 41 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.257 Fit side-chains REVERT: A 181 ARG cc_start: 0.8546 (ptp90) cc_final: 0.8256 (ptp90) REVERT: A 234 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7444 (pp) REVERT: A 281 VAL cc_start: 0.9230 (t) cc_final: 0.8999 (p) outliers start: 7 outliers final: 4 residues processed: 40 average time/residue: 0.1249 time to fit residues: 6.1517 Evaluate side-chains 35 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 234 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 25 optimal weight: 9.9990 chunk 27 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 17 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4130 r_free = 0.4130 target = 0.127997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.087489 restraints weight = 6171.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.089659 restraints weight = 2963.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.090838 restraints weight = 1849.652| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2297 Z= 0.170 Angle : 0.553 9.639 3108 Z= 0.289 Chirality : 0.038 0.111 363 Planarity : 0.003 0.025 403 Dihedral : 3.956 25.903 311 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.97 % Allowed : 16.95 % 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: 3.02 (0.48), residues: 292 helix: 2.55 (0.34), residues: 216 sheet: None (None), residues: 0 loop : 0.40 (0.67), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 206 HIS 0.010 0.002 HIS A 193 PHE 0.004 0.001 PHE A 103 TYR 0.006 0.001 TYR A 252 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 37 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.253 Fit side-chains REVERT: A 77 GLU cc_start: 0.8127 (tp30) cc_final: 0.7820 (tm-30) REVERT: A 181 ARG cc_start: 0.8561 (ptp90) cc_final: 0.8284 (ptp90) REVERT: A 250 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7972 (mt) REVERT: A 281 VAL cc_start: 0.9216 (t) cc_final: 0.8905 (p) outliers start: 7 outliers final: 4 residues processed: 36 average time/residue: 0.1130 time to fit residues: 5.1277 Evaluate side-chains 35 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 250 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 3 optimal weight: 0.7980 chunk 20 optimal weight: 20.0000 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.4124 r_free = 0.4124 target = 0.127524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.086966 restraints weight = 6388.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.089131 restraints weight = 3029.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.090433 restraints weight = 1877.494| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2297 Z= 0.182 Angle : 0.580 9.443 3108 Z= 0.295 Chirality : 0.039 0.111 363 Planarity : 0.003 0.026 403 Dihedral : 3.916 25.100 311 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.81 % Allowed : 16.10 % 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: 2.97 (0.47), residues: 292 helix: 2.54 (0.34), residues: 216 sheet: None (None), residues: 0 loop : 0.31 (0.67), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 206 HIS 0.011 0.002 HIS A 193 PHE 0.005 0.001 PHE A 136 TYR 0.007 0.001 TYR A 252 ARG 0.001 0.000 ARG A 124 *********************** 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 41 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.309 Fit side-chains REVERT: A 181 ARG cc_start: 0.8541 (ptp90) cc_final: 0.8267 (ptp90) REVERT: A 250 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8211 (mt) REVERT: A 281 VAL cc_start: 0.9255 (t) cc_final: 0.8965 (p) outliers start: 9 outliers final: 6 residues processed: 40 average time/residue: 0.1218 time to fit residues: 6.2191 Evaluate side-chains 38 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain A residue 250 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 16 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 28 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.4122 r_free = 0.4122 target = 0.127779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.087161 restraints weight = 6145.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.089326 restraints weight = 2915.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.090635 restraints weight = 1816.832| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2297 Z= 0.177 Angle : 0.591 9.113 3108 Z= 0.304 Chirality : 0.039 0.109 363 Planarity : 0.003 0.025 403 Dihedral : 3.937 25.954 311 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.97 % Allowed : 17.37 % Favored : 79.66 % 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: 2.98 (0.47), residues: 292 helix: 2.58 (0.34), residues: 215 sheet: None (None), residues: 0 loop : 0.22 (0.66), 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 0.004 0.001 PHE A 103 TYR 0.007 0.001 TYR A 252 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 38 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.275 Fit side-chains REVERT: A 181 ARG cc_start: 0.8555 (ptp90) cc_final: 0.8289 (ptp90) REVERT: A 250 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8189 (mt) REVERT: A 281 VAL cc_start: 0.9254 (t) cc_final: 0.8971 (p) outliers start: 7 outliers final: 5 residues processed: 37 average time/residue: 0.1126 time to fit residues: 5.2662 Evaluate side-chains 37 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 133 THR Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 250 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 26 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 20 optimal weight: 20.0000 chunk 3 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4121 r_free = 0.4121 target = 0.128006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.087650 restraints weight = 6097.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.089724 restraints weight = 2997.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.090938 restraints weight = 1912.033| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3860 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= 0.180 Angle : 0.600 9.090 3108 Z= 0.310 Chirality : 0.039 0.110 363 Planarity : 0.003 0.025 403 Dihedral : 3.925 25.469 311 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.54 % Allowed : 17.80 % Favored : 79.66 % 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: 2.94 (0.48), residues: 292 helix: 2.52 (0.34), residues: 217 sheet: None (None), residues: 0 loop : 0.28 (0.67), 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 0.004 0.001 PHE A 103 TYR 0.007 0.001 TYR A 252 ARG 0.001 0.000 ARG A 124 ********************** 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 37 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.249 Fit side-chains REVERT: A 250 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8371 (mm) outliers start: 6 outliers final: 4 residues processed: 36 average time/residue: 0.1414 time to fit residues: 6.3002 Evaluate side-chains 35 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.259 ------------------------------------------------------------------------------- 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 250 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 7 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4133 r_free = 0.4133 target = 0.129071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.088644 restraints weight = 5977.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.090810 restraints weight = 2892.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.092122 restraints weight = 1813.707| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3962 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= 0.166 Angle : 0.589 9.045 3108 Z= 0.303 Chirality : 0.039 0.110 363 Planarity : 0.003 0.025 403 Dihedral : 3.908 25.479 311 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.97 % Allowed : 17.80 % Favored : 79.24 % 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: 2.86 (0.48), residues: 292 helix: 2.49 (0.34), residues: 217 sheet: None (None), residues: 0 loop : 0.13 (0.68), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 206 HIS 0.011 0.002 HIS A 193 PHE 0.004 0.001 PHE A 154 TYR 0.007 0.001 TYR A 252 ARG 0.001 0.000 ARG A 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1067.59 seconds wall clock time: 20 minutes 13.13 seconds (1213.13 seconds total)