Starting phenix.real_space_refine on Wed Mar 5 15:22:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ve7_43167/03_2025/8ve7_43167.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ve7_43167/03_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_43167/03_2025/8ve7_43167.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ve7_43167/03_2025/8ve7_43167.map" model { file = "/net/cci-nas-00/data/ceres_data/8ve7_43167/03_2025/8ve7_43167.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ve7_43167/03_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-5624/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: 2.21, 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: 0.59 Conformation dependent library (CDL) restraints added in 287.3 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: 0.22 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: 0.54 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: 0.980 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.040 Process input model: 11.030 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 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 : 0.302 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: 0.1758 time to fit residues: 12.3608 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 : 0.263 ------------------------------------------------------------------------------- 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: 0.6980 chunk 22 optimal weight: 0.9990 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: 0.8584 ------------------------------------------------------------------------------- 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 = 0.4108 r_free = 0.4108 target = 0.127953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.087129 restraints weight = 6086.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.089436 restraints weight = 2970.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.090752 restraints weight = 1843.659| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2297 Z= 0.177 Angle : 0.544 5.998 3108 Z= 0.285 Chirality : 0.038 0.118 363 Planarity : 0.003 0.018 403 Dihedral : 4.009 24.763 311 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.54 % Allowed : 7.20 % Favored : 90.25 % 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: 3.14 (0.47), residues: 292 helix: 2.47 (0.33), residues: 216 sheet: None (None), residues: 0 loop : 1.06 (0.72), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 86 HIS 0.004 0.001 HIS A 209 PHE 0.019 0.001 PHE A 103 TYR 0.005 0.001 TYR A 252 ARG 0.003 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 42 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.234 Fit side-chains REVERT: A 193 HIS cc_start: 0.9078 (p90) cc_final: 0.8861 (p-80) REVERT: A 206 TRP cc_start: 0.8378 (t60) cc_final: 0.8161 (t60) REVERT: A 257 ASN cc_start: 0.7944 (m-40) cc_final: 0.7735 (m110) outliers start: 6 outliers final: 2 residues processed: 40 average time/residue: 0.1081 time to fit residues: 5.4531 Evaluate side-chains 33 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU 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: 1.9990 chunk 16 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.4098 r_free = 0.4098 target = 0.126052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.084981 restraints weight = 5972.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.087031 restraints weight = 3004.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.088270 restraints weight = 1938.482| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2297 Z= 0.256 Angle : 0.577 6.907 3108 Z= 0.301 Chirality : 0.039 0.112 363 Planarity : 0.003 0.025 403 Dihedral : 3.929 25.426 311 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.97 % Allowed : 11.02 % Favored : 86.02 % 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: 3.04 (0.47), residues: 292 helix: 2.45 (0.33), residues: 216 sheet: None (None), residues: 0 loop : 0.84 (0.71), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 86 HIS 0.004 0.001 HIS A 209 PHE 0.014 0.001 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 40 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.282 Fit side-chains REVERT: A 181 ARG cc_start: 0.8635 (ptp90) cc_final: 0.8374 (ptp90) REVERT: A 257 ASN cc_start: 0.8090 (m-40) cc_final: 0.7858 (m110) outliers start: 7 outliers final: 4 residues processed: 38 average time/residue: 0.1133 time to fit residues: 5.5137 Evaluate side-chains 35 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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: 4.9990 chunk 19 optimal weight: 0.4980 chunk 26 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 2 optimal weight: 0.0770 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS A 242 HIS ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.127428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.086832 restraints weight = 6038.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.088964 restraints weight = 2936.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.090209 restraints weight = 1830.834| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2297 Z= 0.190 Angle : 0.536 5.879 3108 Z= 0.290 Chirality : 0.038 0.112 363 Planarity : 0.003 0.026 403 Dihedral : 3.990 25.630 311 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.54 % Allowed : 12.71 % Favored : 84.75 % 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: 3.14 (0.48), residues: 292 helix: 2.53 (0.34), residues: 216 sheet: None (None), residues: 0 loop : 0.83 (0.71), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 206 HIS 0.003 0.001 HIS A 202 PHE 0.012 0.001 PHE A 103 TYR 0.007 0.001 TYR A 64 ARG 0.002 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 37 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.198 Fit side-chains REVERT: A 181 ARG cc_start: 0.8595 (ptp90) cc_final: 0.8341 (ptp90) REVERT: A 257 ASN cc_start: 0.7915 (m-40) cc_final: 0.7713 (m110) outliers start: 6 outliers final: 3 residues processed: 36 average time/residue: 0.1055 time to fit residues: 4.7995 Evaluate side-chains 33 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 14 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.127072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.086779 restraints weight = 6157.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.088863 restraints weight = 2962.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.090140 restraints weight = 1848.952| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2297 Z= 0.187 Angle : 0.534 7.940 3108 Z= 0.280 Chirality : 0.039 0.119 363 Planarity : 0.003 0.027 403 Dihedral : 3.975 25.956 311 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.12 % Allowed : 13.98 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.09 (0.48), residues: 292 helix: 2.51 (0.34), residues: 216 sheet: None (None), residues: 0 loop : 0.76 (0.71), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 206 HIS 0.005 0.001 HIS A 235 PHE 0.011 0.001 PHE A 103 TYR 0.009 0.001 TYR A 145 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 37 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.255 Fit side-chains REVERT: A 181 ARG cc_start: 0.8587 (ptp90) cc_final: 0.8338 (ptp90) REVERT: A 257 ASN cc_start: 0.7879 (m-40) cc_final: 0.7664 (m110) outliers start: 5 outliers final: 3 residues processed: 36 average time/residue: 0.1106 time to fit residues: 5.0889 Evaluate side-chains 33 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 7 optimal weight: 0.4980 chunk 18 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 HIS A 242 HIS ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.127678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.086877 restraints weight = 6101.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.089085 restraints weight = 2892.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.090349 restraints weight = 1783.571| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3502 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= 0.162 Angle : 0.551 11.138 3108 Z= 0.277 Chirality : 0.039 0.109 363 Planarity : 0.003 0.028 403 Dihedral : 3.986 25.393 311 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.69 % Allowed : 17.80 % Favored : 80.51 % 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: 2.48 (0.34), residues: 216 sheet: None (None), residues: 0 loop : 0.59 (0.70), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 206 HIS 0.008 0.002 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 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 38 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.258 Fit side-chains REVERT: A 181 ARG cc_start: 0.8563 (ptp90) cc_final: 0.8303 (ptp90) REVERT: A 257 ASN cc_start: 0.7888 (m-40) cc_final: 0.7665 (m110) outliers start: 4 outliers final: 2 residues processed: 37 average time/residue: 0.1298 time to fit residues: 5.9299 Evaluate side-chains 34 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 155 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 25 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 12 optimal weight: 0.7980 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.4119 r_free = 0.4119 target = 0.127063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.086401 restraints weight = 6119.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.088494 restraints weight = 2974.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.089751 restraints weight = 1863.223| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3622 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= 0.200 Angle : 0.579 9.598 3108 Z= 0.296 Chirality : 0.039 0.152 363 Planarity : 0.003 0.029 403 Dihedral : 3.926 25.599 311 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 4.24 % Allowed : 17.37 % 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: 2.97 (0.48), residues: 292 helix: 2.49 (0.34), residues: 216 sheet: None (None), residues: 0 loop : 0.47 (0.69), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 206 HIS 0.009 0.002 HIS A 193 PHE 0.010 0.001 PHE A 103 TYR 0.007 0.001 TYR A 252 ARG 0.002 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 43 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.239 Fit side-chains REVERT: A 77 GLU cc_start: 0.8112 (tp30) cc_final: 0.7897 (tm-30) REVERT: A 181 ARG cc_start: 0.8604 (ptp90) cc_final: 0.8365 (ptp90) REVERT: A 250 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8289 (mm) REVERT: A 257 ASN cc_start: 0.7821 (m-40) cc_final: 0.7587 (m110) REVERT: A 281 VAL cc_start: 0.9264 (t) cc_final: 0.8999 (p) outliers start: 10 outliers final: 6 residues processed: 42 average time/residue: 0.1240 time to fit residues: 6.5254 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 : 0.235 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 28 optimal weight: 8.9990 chunk 2 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.4102 r_free = 0.4102 target = 0.126306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.086324 restraints weight = 6330.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.088505 restraints weight = 2955.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.089777 restraints weight = 1813.245| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2297 Z= 0.207 Angle : 0.617 11.008 3108 Z= 0.310 Chirality : 0.040 0.170 363 Planarity : 0.003 0.030 403 Dihedral : 4.008 25.675 311 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 4.66 % Allowed : 16.53 % 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: 2.96 (0.48), residues: 292 helix: 2.49 (0.34), residues: 216 sheet: None (None), residues: 0 loop : 0.47 (0.69), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 206 HIS 0.011 0.003 HIS A 209 PHE 0.011 0.001 PHE A 103 TYR 0.018 0.002 TYR A 145 ARG 0.002 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 42 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.255 Fit side-chains REVERT: A 250 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8400 (mm) REVERT: A 257 ASN cc_start: 0.8020 (m-40) cc_final: 0.7783 (m110) REVERT: A 281 VAL cc_start: 0.9266 (t) cc_final: 0.9065 (p) outliers start: 11 outliers final: 8 residues processed: 41 average time/residue: 0.1098 time to fit residues: 5.7240 Evaluate side-chains 38 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 87 LEU 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 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 16 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 18 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 26 optimal weight: 0.1980 chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.128237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.088211 restraints weight = 6092.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.090408 restraints weight = 2917.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.091724 restraints weight = 1807.062| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3980 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= 0.165 Angle : 0.607 10.763 3108 Z= 0.306 Chirality : 0.040 0.144 363 Planarity : 0.003 0.030 403 Dihedral : 4.025 26.731 311 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.39 % Allowed : 18.64 % 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: 3.02 (0.48), residues: 292 helix: 2.54 (0.34), residues: 215 sheet: None (None), residues: 0 loop : 0.48 (0.69), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 206 HIS 0.012 0.003 HIS A 209 PHE 0.010 0.001 PHE A 103 TYR 0.018 0.002 TYR A 145 ARG 0.001 0.000 ARG A 83 *********************** 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 44 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.243 Fit side-chains REVERT: A 181 ARG cc_start: 0.8739 (ptp90) cc_final: 0.8467 (ptp90) REVERT: A 257 ASN cc_start: 0.7971 (m-40) cc_final: 0.7681 (m110) REVERT: A 281 VAL cc_start: 0.9251 (t) cc_final: 0.9051 (p) outliers start: 8 outliers final: 4 residues processed: 43 average time/residue: 0.1147 time to fit residues: 6.2236 Evaluate side-chains 38 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 91 ILE 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 26 optimal weight: 0.0010 chunk 22 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 20 optimal weight: 20.0000 chunk 3 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 overall best weight: 0.6786 ------------------------------------------------------------------------------- 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 = 0.4128 r_free = 0.4128 target = 0.128718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.088548 restraints weight = 6030.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.090681 restraints weight = 2906.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.091969 restraints weight = 1834.021| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.4055 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= 0.184 Angle : 0.670 10.876 3108 Z= 0.333 Chirality : 0.042 0.248 363 Planarity : 0.003 0.030 403 Dihedral : 4.051 26.636 311 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % 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: 3.03 (0.48), residues: 292 helix: 2.53 (0.34), residues: 217 sheet: None (None), residues: 0 loop : 0.51 (0.69), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 206 HIS 0.011 0.003 HIS A 193 PHE 0.010 0.001 PHE A 103 TYR 0.017 0.002 TYR A 145 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 41 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.238 Fit side-chains REVERT: A 57 GLU cc_start: 0.7513 (tm-30) cc_final: 0.6949 (tm-30) REVERT: A 257 ASN cc_start: 0.7938 (m-40) cc_final: 0.7680 (m110) outliers start: 6 outliers final: 5 residues processed: 41 average time/residue: 0.1111 time to fit residues: 5.7279 Evaluate side-chains 39 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU 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 269 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 7 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 0.0770 chunk 9 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 = 0.4138 r_free = 0.4138 target = 0.129650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.089828 restraints weight = 6063.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.091863 restraints weight = 3024.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.093019 restraints weight = 1930.878| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2297 Z= 0.191 Angle : 0.735 14.394 3108 Z= 0.354 Chirality : 0.048 0.481 363 Planarity : 0.003 0.030 403 Dihedral : 4.070 26.520 311 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.46 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: 2.94 (0.48), residues: 292 helix: 2.49 (0.34), residues: 217 sheet: None (None), residues: 0 loop : 0.38 (0.69), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 206 HIS 0.012 0.003 HIS A 193 PHE 0.010 0.001 PHE A 103 TYR 0.016 0.001 TYR A 145 ARG 0.001 0.000 ARG A 124 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1185.94 seconds wall clock time: 21 minutes 7.02 seconds (1267.02 seconds total)