Starting phenix.real_space_refine on Fri May 9 13:48:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w8s_37358/05_2025/8w8s_37358.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w8s_37358/05_2025/8w8s_37358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w8s_37358/05_2025/8w8s_37358.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w8s_37358/05_2025/8w8s_37358.map" model { file = "/net/cci-nas-00/data/ceres_data/8w8s_37358/05_2025/8w8s_37358.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w8s_37358/05_2025/8w8s_37358.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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: 5 Type Number sf(0) Gaussians S 15 5.16 5 C 1524 2.51 5 N 363 2.21 5 O 357 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 2265 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2223 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 13, 'TRANS': 267} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "R" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'U7D': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.28, per 1000 atoms: 1.01 Number of scatterers: 2265 At special positions: 0 Unit cell: (56.95, 69.7, 71.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 F 6 9.00 O 357 8.00 N 363 7.00 C 1524 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 104 " - pdb=" SG CYS R 182 " distance=2.04 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 278.9 milliseconds 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 544 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 0 sheets defined 79.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'R' and resid 27 through 58 removed outlier: 3.717A pdb=" N VAL R 39 " --> pdb=" O SER R 35 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE R 40 " --> pdb=" O THR R 36 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE R 41 " --> pdb=" O VAL R 37 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU R 42 " --> pdb=" O LEU R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 91 Proline residue: R 86 - end of helix Processing helix chain 'R' and resid 100 through 134 removed outlier: 3.861A pdb=" N CYS R 104 " --> pdb=" O ASN R 100 " (cutoff:3.500A) Processing helix chain 'R' and resid 144 through 162 Processing helix chain 'R' and resid 189 through 201 Processing helix chain 'R' and resid 201 through 228 removed outlier: 4.060A pdb=" N VAL R 214 " --> pdb=" O ALA R 210 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL R 215 " --> pdb=" O CYS R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 396 through 425 removed outlier: 4.199A pdb=" N VAL R 400 " --> pdb=" O LYS R 396 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE R 401 " --> pdb=" O ALA R 397 " (cutoff:3.500A) Proline residue: R 414 - end of helix removed outlier: 3.904A pdb=" N VAL R 423 " --> pdb=" O ALA R 419 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TRP R 424 " --> pdb=" O VAL R 420 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL R 425 " --> pdb=" O LEU R 421 " (cutoff:3.500A) Processing helix chain 'R' and resid 432 through 444 removed outlier: 3.624A pdb=" N ILE R 436 " --> pdb=" O PRO R 432 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE R 444 " --> pdb=" O ILE R 440 " (cutoff:3.500A) Processing helix chain 'R' and resid 445 through 455 Proline residue: R 451 - end of helix Processing helix chain 'R' and resid 458 through 473 160 hydrogen bonds defined for protein. 480 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: 0.55 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: 635 1.34 - 1.46: 462 1.46 - 1.58: 1214 1.58 - 1.70: 2 1.70 - 1.82: 18 Bond restraints: 2331 Sorted by residual: bond pdb=" C07 U7D R 601 " pdb=" N02 U7D R 601 " ideal model delta sigma weight residual 1.353 1.453 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" C07 U7D R 602 " pdb=" N02 U7D R 602 " ideal model delta sigma weight residual 1.353 1.452 -0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" C07 U7D R 602 " pdb=" N03 U7D R 602 " ideal model delta sigma weight residual 1.359 1.453 -0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" C07 U7D R 601 " pdb=" N03 U7D R 601 " ideal model delta sigma weight residual 1.359 1.450 -0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C07 U7D R 602 " pdb=" S01 U7D R 602 " ideal model delta sigma weight residual 1.685 1.597 0.088 2.00e-02 2.50e+03 1.95e+01 ... (remaining 2326 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 3069 2.05 - 4.11: 99 4.11 - 6.16: 18 6.16 - 8.21: 4 8.21 - 10.27: 4 Bond angle restraints: 3194 Sorted by residual: angle pdb=" N ASN R 179 " pdb=" CA ASN R 179 " pdb=" C ASN R 179 " ideal model delta sigma weight residual 114.31 107.81 6.50 1.29e+00 6.01e-01 2.54e+01 angle pdb=" C LEU R 63 " pdb=" CA LEU R 63 " pdb=" CB LEU R 63 " ideal model delta sigma weight residual 116.63 111.88 4.75 1.16e+00 7.43e-01 1.68e+01 angle pdb=" CA GLN R 61 " pdb=" C GLN R 61 " pdb=" O GLN R 61 " ideal model delta sigma weight residual 122.64 118.33 4.31 1.25e+00 6.40e-01 1.19e+01 angle pdb=" C03 U7D R 602 " pdb=" N02 U7D R 602 " pdb=" C07 U7D R 602 " ideal model delta sigma weight residual 131.23 120.96 10.27 3.00e+00 1.11e-01 1.17e+01 angle pdb=" C07 U7D R 601 " pdb=" N03 U7D R 601 " pdb=" C08 U7D R 601 " ideal model delta sigma weight residual 129.10 119.10 10.00 3.00e+00 1.11e-01 1.11e+01 ... (remaining 3189 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.80: 1122 16.80 - 33.60: 171 33.60 - 50.40: 39 50.40 - 67.20: 5 67.20 - 84.01: 1 Dihedral angle restraints: 1338 sinusoidal: 502 harmonic: 836 Sorted by residual: dihedral pdb=" CB CYS R 104 " pdb=" SG CYS R 104 " pdb=" SG CYS R 182 " pdb=" CB CYS R 182 " ideal model delta sinusoidal sigma weight residual -86.00 -20.68 -65.32 1 1.00e+01 1.00e-02 5.59e+01 dihedral pdb=" CA THR R 164 " pdb=" C THR R 164 " pdb=" N PRO R 165 " pdb=" CA PRO R 165 " ideal model delta harmonic sigma weight residual 180.00 156.45 23.55 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" C PHE R 96 " pdb=" N PHE R 96 " pdb=" CA PHE R 96 " pdb=" CB PHE R 96 " ideal model delta harmonic sigma weight residual -122.60 -131.31 8.71 0 2.50e+00 1.60e-01 1.21e+01 ... (remaining 1335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 278 0.045 - 0.090: 77 0.090 - 0.136: 21 0.136 - 0.181: 6 0.181 - 0.226: 1 Chirality restraints: 383 Sorted by residual: chirality pdb=" CA PHE R 96 " pdb=" N PHE R 96 " pdb=" C PHE R 96 " pdb=" CB PHE R 96 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB VAL R 65 " pdb=" CA VAL R 65 " pdb=" CG1 VAL R 65 " pdb=" CG2 VAL R 65 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.41e-01 chirality pdb=" CA MET R 184 " pdb=" N MET R 184 " pdb=" C MET R 184 " pdb=" CB MET R 184 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.85e-01 ... (remaining 380 not shown) Planarity restraints: 375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR R 164 " -0.058 5.00e-02 4.00e+02 8.76e-02 1.23e+01 pdb=" N PRO R 165 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO R 165 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO R 165 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 413 " -0.023 5.00e-02 4.00e+02 3.46e-02 1.91e+00 pdb=" N PRO R 414 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO R 414 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO R 414 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO R 165 " 0.022 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO R 166 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO R 166 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 166 " 0.018 5.00e-02 4.00e+02 ... (remaining 372 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 697 2.83 - 3.35: 2235 3.35 - 3.86: 3522 3.86 - 4.38: 3405 4.38 - 4.90: 6439 Nonbonded interactions: 16298 Sorted by model distance: nonbonded pdb=" O THR R 164 " pdb=" OG1 THR R 164 " model vdw 2.310 3.040 nonbonded pdb=" OD1 ASP R 176 " pdb=" N LEU R 181 " model vdw 2.446 3.120 nonbonded pdb=" O SER R 45 " pdb=" ND2 ASN R 49 " model vdw 2.448 3.120 nonbonded pdb=" O LEU R 62 " pdb=" ND2 ASN R 67 " model vdw 2.478 3.120 nonbonded pdb=" OD1 ASN R 72 " pdb=" OG1 THR R 121 " model vdw 2.510 3.040 ... (remaining 16293 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.320 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.970 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 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 : 0.007 0.100 2332 Z= 0.414 Angle : 0.889 10.268 3196 Z= 0.518 Chirality : 0.047 0.226 383 Planarity : 0.006 0.088 375 Dihedral : 16.080 84.006 791 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.64 % Allowed : 22.95 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.52), residues: 277 helix: 2.25 (0.36), residues: 202 sheet: None (None), residues: 0 loop : -2.60 (0.68), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 441 HIS 0.001 0.000 HIS R 135 PHE 0.011 0.001 PHE R 200 TYR 0.009 0.001 TYR R 454 ARG 0.003 0.000 ARG R 178 Details of bonding type rmsd hydrogen bonds : bond 0.10114 ( 160) hydrogen bonds : angle 4.48709 ( 480) SS BOND : bond 0.01114 ( 1) SS BOND : angle 1.64860 ( 2) covalent geometry : bond 0.00697 ( 2331) covalent geometry : angle 0.88872 ( 3194) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.249 Fit side-chains REVERT: R 79 LEU cc_start: 0.7987 (mp) cc_final: 0.7670 (mp) REVERT: R 97 TRP cc_start: 0.8799 (t-100) cc_final: 0.8335 (m-90) REVERT: R 457 MET cc_start: 0.8773 (mtp) cc_final: 0.8542 (mtp) outliers start: 4 outliers final: 1 residues processed: 32 average time/residue: 0.1446 time to fit residues: 5.5946 Evaluate side-chains 28 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 99 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 13 optimal weight: 0.0060 chunk 16 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- 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 = 0.3457 r_free = 0.3457 target = 0.094001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.078020 restraints weight = 5153.518| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.87 r_work: 0.3079 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.0659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2332 Z= 0.121 Angle : 0.538 6.180 3196 Z= 0.276 Chirality : 0.041 0.192 383 Planarity : 0.006 0.073 375 Dihedral : 4.966 43.372 315 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.46 % Allowed : 21.72 % Favored : 75.82 % 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: 2.18 (0.52), residues: 277 helix: 2.74 (0.35), residues: 203 sheet: None (None), residues: 0 loop : -2.55 (0.69), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 441 HIS 0.001 0.000 HIS R 135 PHE 0.014 0.001 PHE R 96 TYR 0.009 0.001 TYR R 454 ARG 0.003 0.000 ARG R 221 Details of bonding type rmsd hydrogen bonds : bond 0.04050 ( 160) hydrogen bonds : angle 3.71974 ( 480) SS BOND : bond 0.00604 ( 1) SS BOND : angle 2.19789 ( 2) covalent geometry : bond 0.00262 ( 2331) covalent geometry : angle 0.53516 ( 3194) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.242 Fit side-chains REVERT: R 97 TRP cc_start: 0.8786 (t-100) cc_final: 0.8293 (m-90) REVERT: R 457 MET cc_start: 0.8896 (mtp) cc_final: 0.8688 (mtp) outliers start: 6 outliers final: 5 residues processed: 33 average time/residue: 0.1096 time to fit residues: 4.6739 Evaluate side-chains 31 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 200 PHE Chi-restraints excluded: chain R residue 468 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 10 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 24 optimal weight: 0.0000 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- 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 = 0.3440 r_free = 0.3440 target = 0.092711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.076705 restraints weight = 5143.906| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.83 r_work: 0.3067 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2332 Z= 0.119 Angle : 0.529 5.663 3196 Z= 0.269 Chirality : 0.041 0.191 383 Planarity : 0.005 0.069 375 Dihedral : 3.642 23.569 313 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.69 % Allowed : 21.31 % Favored : 75.00 % 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: 2.30 (0.52), residues: 277 helix: 2.79 (0.35), residues: 205 sheet: None (None), residues: 0 loop : -2.54 (0.67), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 441 HIS 0.001 0.000 HIS R 135 PHE 0.010 0.001 PHE R 96 TYR 0.008 0.001 TYR R 454 ARG 0.003 0.000 ARG R 221 Details of bonding type rmsd hydrogen bonds : bond 0.04040 ( 160) hydrogen bonds : angle 3.60571 ( 480) SS BOND : bond 0.00202 ( 1) SS BOND : angle 2.08405 ( 2) covalent geometry : bond 0.00273 ( 2331) covalent geometry : angle 0.52630 ( 3194) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.260 Fit side-chains REVERT: R 457 MET cc_start: 0.8921 (mtp) cc_final: 0.8717 (mtp) outliers start: 9 outliers final: 5 residues processed: 36 average time/residue: 0.1322 time to fit residues: 5.8894 Evaluate side-chains 33 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 200 PHE Chi-restraints excluded: chain R residue 468 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 8 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 24 optimal weight: 0.0670 chunk 1 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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 = 0.3455 r_free = 0.3455 target = 0.093650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.077725 restraints weight = 5101.697| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.84 r_work: 0.3088 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 2332 Z= 0.111 Angle : 0.548 9.656 3196 Z= 0.268 Chirality : 0.041 0.198 383 Planarity : 0.005 0.065 375 Dihedral : 3.575 22.800 313 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.46 % Allowed : 24.18 % Favored : 73.36 % 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: 2.44 (0.52), residues: 277 helix: 2.91 (0.35), residues: 205 sheet: None (None), residues: 0 loop : -2.55 (0.67), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 441 HIS 0.001 0.000 HIS R 135 PHE 0.009 0.001 PHE R 96 TYR 0.009 0.001 TYR R 454 ARG 0.002 0.000 ARG R 221 Details of bonding type rmsd hydrogen bonds : bond 0.03698 ( 160) hydrogen bonds : angle 3.56052 ( 480) SS BOND : bond 0.00214 ( 1) SS BOND : angle 1.76287 ( 2) covalent geometry : bond 0.00250 ( 2331) covalent geometry : angle 0.54624 ( 3194) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.233 Fit side-chains REVERT: R 457 MET cc_start: 0.8873 (mtp) cc_final: 0.8665 (mtp) outliers start: 6 outliers final: 3 residues processed: 37 average time/residue: 0.1256 time to fit residues: 5.6932 Evaluate side-chains 32 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 468 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 0.9990 chunk 13 optimal weight: 0.0270 chunk 8 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 chunk 9 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 3 optimal weight: 6.9990 overall best weight: 0.5842 ------------------------------------------------------------------------------- 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 = 0.3467 r_free = 0.3467 target = 0.094290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.078483 restraints weight = 5156.274| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.84 r_work: 0.3088 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 2332 Z= 0.110 Angle : 0.546 9.441 3196 Z= 0.267 Chirality : 0.041 0.196 383 Planarity : 0.005 0.062 375 Dihedral : 3.544 22.417 313 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.05 % Allowed : 27.05 % Favored : 70.90 % 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: 2.54 (0.52), residues: 277 helix: 2.99 (0.35), residues: 206 sheet: None (None), residues: 0 loop : -2.65 (0.67), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 441 HIS 0.001 0.000 HIS R 135 PHE 0.009 0.001 PHE R 200 TYR 0.009 0.001 TYR R 454 ARG 0.001 0.000 ARG R 221 Details of bonding type rmsd hydrogen bonds : bond 0.03533 ( 160) hydrogen bonds : angle 3.51464 ( 480) SS BOND : bond 0.00165 ( 1) SS BOND : angle 1.56669 ( 2) covalent geometry : bond 0.00244 ( 2331) covalent geometry : angle 0.54449 ( 3194) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.231 Fit side-chains REVERT: R 457 MET cc_start: 0.8875 (mtp) cc_final: 0.8666 (mtp) outliers start: 5 outliers final: 1 residues processed: 34 average time/residue: 0.1307 time to fit residues: 5.4305 Evaluate side-chains 29 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 0.3980 chunk 4 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3458 r_free = 0.3458 target = 0.093732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.077871 restraints weight = 5121.246| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.82 r_work: 0.3094 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2332 Z= 0.114 Angle : 0.554 9.779 3196 Z= 0.270 Chirality : 0.041 0.203 383 Planarity : 0.005 0.061 375 Dihedral : 3.601 22.147 313 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.05 % Allowed : 26.64 % Favored : 71.31 % 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: 2.61 (0.52), residues: 277 helix: 3.05 (0.34), residues: 206 sheet: None (None), residues: 0 loop : -2.63 (0.68), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 170 HIS 0.001 0.000 HIS R 135 PHE 0.007 0.001 PHE R 200 TYR 0.009 0.001 TYR R 454 ARG 0.001 0.000 ARG R 221 Details of bonding type rmsd hydrogen bonds : bond 0.03548 ( 160) hydrogen bonds : angle 3.50211 ( 480) SS BOND : bond 0.00116 ( 1) SS BOND : angle 1.51165 ( 2) covalent geometry : bond 0.00265 ( 2331) covalent geometry : angle 0.55256 ( 3194) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.237 Fit side-chains REVERT: R 457 MET cc_start: 0.8880 (mtp) cc_final: 0.8664 (mtp) outliers start: 5 outliers final: 2 residues processed: 35 average time/residue: 0.1270 time to fit residues: 5.4368 Evaluate side-chains 30 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 38 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 430 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.093286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.077280 restraints weight = 5192.944| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.85 r_work: 0.3077 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2332 Z= 0.115 Angle : 0.565 9.495 3196 Z= 0.275 Chirality : 0.042 0.206 383 Planarity : 0.005 0.061 375 Dihedral : 3.639 22.416 313 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.64 % Allowed : 26.64 % Favored : 71.72 % 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: 2.62 (0.52), residues: 277 helix: 3.11 (0.34), residues: 205 sheet: None (None), residues: 0 loop : -2.73 (0.66), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 170 HIS 0.001 0.000 HIS R 135 PHE 0.011 0.001 PHE R 200 TYR 0.009 0.001 TYR R 454 ARG 0.001 0.000 ARG R 221 Details of bonding type rmsd hydrogen bonds : bond 0.03671 ( 160) hydrogen bonds : angle 3.47400 ( 480) SS BOND : bond 0.00055 ( 1) SS BOND : angle 1.73596 ( 2) covalent geometry : bond 0.00269 ( 2331) covalent geometry : angle 0.56375 ( 3194) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.244 Fit side-chains REVERT: R 457 MET cc_start: 0.8870 (mtp) cc_final: 0.8648 (mtp) outliers start: 4 outliers final: 2 residues processed: 33 average time/residue: 0.1353 time to fit residues: 5.5306 Evaluate side-chains 30 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 182 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 19 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 0.0050 chunk 5 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- 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 = 0.3459 r_free = 0.3459 target = 0.093875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.077849 restraints weight = 5293.071| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.88 r_work: 0.3089 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2332 Z= 0.113 Angle : 0.561 9.539 3196 Z= 0.272 Chirality : 0.041 0.213 383 Planarity : 0.005 0.060 375 Dihedral : 3.652 22.100 313 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.05 % Allowed : 26.23 % Favored : 71.72 % 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: 2.64 (0.52), residues: 277 helix: 3.13 (0.34), residues: 205 sheet: None (None), residues: 0 loop : -2.73 (0.66), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 170 HIS 0.001 0.000 HIS R 135 PHE 0.009 0.001 PHE R 200 TYR 0.010 0.001 TYR R 454 ARG 0.001 0.000 ARG R 221 Details of bonding type rmsd hydrogen bonds : bond 0.03514 ( 160) hydrogen bonds : angle 3.45117 ( 480) SS BOND : bond 0.00174 ( 1) SS BOND : angle 1.67991 ( 2) covalent geometry : bond 0.00257 ( 2331) covalent geometry : angle 0.55924 ( 3194) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.248 Fit side-chains REVERT: R 457 MET cc_start: 0.8857 (mtp) cc_final: 0.8639 (mtp) outliers start: 5 outliers final: 2 residues processed: 34 average time/residue: 0.1353 time to fit residues: 5.6630 Evaluate side-chains 30 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 412 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 0.0570 chunk 16 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 0.0870 overall best weight: 0.4876 ------------------------------------------------------------------------------- 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 = 0.3488 r_free = 0.3488 target = 0.095610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.079765 restraints weight = 5126.442| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.85 r_work: 0.3114 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2332 Z= 0.111 Angle : 0.558 9.529 3196 Z= 0.270 Chirality : 0.042 0.218 383 Planarity : 0.005 0.058 375 Dihedral : 3.652 21.588 313 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.82 % Allowed : 27.87 % Favored : 71.31 % 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: 2.66 (0.52), residues: 277 helix: 3.17 (0.34), residues: 204 sheet: None (None), residues: 0 loop : -2.73 (0.65), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 441 HIS 0.001 0.000 HIS R 135 PHE 0.009 0.001 PHE R 200 TYR 0.010 0.001 TYR R 454 ARG 0.001 0.000 ARG R 221 Details of bonding type rmsd hydrogen bonds : bond 0.03327 ( 160) hydrogen bonds : angle 3.41576 ( 480) SS BOND : bond 0.00148 ( 1) SS BOND : angle 1.65079 ( 2) covalent geometry : bond 0.00252 ( 2331) covalent geometry : angle 0.55637 ( 3194) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.253 Fit side-chains REVERT: R 457 MET cc_start: 0.8836 (mtp) cc_final: 0.8630 (mtp) outliers start: 2 outliers final: 1 residues processed: 32 average time/residue: 0.1292 time to fit residues: 5.1005 Evaluate side-chains 30 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 0.0980 chunk 20 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 17 optimal weight: 0.0980 chunk 8 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 = 0.3458 r_free = 0.3458 target = 0.094035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.077621 restraints weight = 5202.341| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.92 r_work: 0.3087 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2332 Z= 0.111 Angle : 0.559 9.416 3196 Z= 0.270 Chirality : 0.041 0.216 383 Planarity : 0.005 0.056 375 Dihedral : 3.643 21.708 313 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.23 % Allowed : 27.46 % Favored : 71.31 % 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: 2.68 (0.52), residues: 277 helix: 3.18 (0.34), residues: 204 sheet: None (None), residues: 0 loop : -2.70 (0.65), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 441 HIS 0.001 0.000 HIS R 135 PHE 0.009 0.001 PHE R 200 TYR 0.010 0.001 TYR R 454 ARG 0.001 0.000 ARG R 221 Details of bonding type rmsd hydrogen bonds : bond 0.03356 ( 160) hydrogen bonds : angle 3.39992 ( 480) SS BOND : bond 0.00097 ( 1) SS BOND : angle 1.64750 ( 2) covalent geometry : bond 0.00255 ( 2331) covalent geometry : angle 0.55722 ( 3194) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.264 Fit side-chains REVERT: R 178 ARG cc_start: 0.9257 (tpt90) cc_final: 0.9032 (ttm-80) REVERT: R 457 MET cc_start: 0.8838 (mtp) cc_final: 0.8617 (mtp) outliers start: 3 outliers final: 1 residues processed: 33 average time/residue: 0.1370 time to fit residues: 5.5725 Evaluate side-chains 29 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 11 optimal weight: 0.0870 chunk 24 optimal weight: 0.3980 chunk 23 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.3465 r_free = 0.3465 target = 0.094342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.077890 restraints weight = 5137.827| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.92 r_work: 0.3094 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2332 Z= 0.110 Angle : 0.556 9.265 3196 Z= 0.270 Chirality : 0.041 0.216 383 Planarity : 0.005 0.056 375 Dihedral : 3.645 21.536 313 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.41 % Allowed : 27.87 % Favored : 71.72 % 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: 2.71 (0.52), residues: 277 helix: 3.18 (0.35), residues: 203 sheet: None (None), residues: 0 loop : -2.52 (0.67), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 170 HIS 0.001 0.000 HIS R 135 PHE 0.009 0.001 PHE R 200 TYR 0.010 0.001 TYR R 454 ARG 0.001 0.000 ARG R 221 Details of bonding type rmsd hydrogen bonds : bond 0.03292 ( 160) hydrogen bonds : angle 3.38660 ( 480) SS BOND : bond 0.00265 ( 1) SS BOND : angle 1.63598 ( 2) covalent geometry : bond 0.00253 ( 2331) covalent geometry : angle 0.55485 ( 3194) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1259.28 seconds wall clock time: 22 minutes 33.67 seconds (1353.67 seconds total)