Starting phenix.real_space_refine on Wed Jun 4 10:51:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w8s_37358/06_2025/8w8s_37358.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w8s_37358/06_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_37358/06_2025/8w8s_37358.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w8s_37358/06_2025/8w8s_37358.map" model { file = "/net/cci-nas-00/data/ceres_data/8w8s_37358/06_2025/8w8s_37358.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w8s_37358/06_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-5710/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: 2.08, per 1000 atoms: 0.92 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: 0.78 Conformation dependent library (CDL) restraints added in 341.9 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: 0.21 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: 0.69 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: 0.340 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.510 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.960 ------------------------------------------------------------------------------- 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 : 0.264 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: 0.1576 time to fit residues: 6.0837 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 : 0.272 ------------------------------------------------------------------------------- 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: 1.9990 chunk 16 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.3429 r_free = 0.3429 target = 0.092897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.076342 restraints weight = 5205.614| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.95 r_work: 0.3033 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.0796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2332 Z= 0.137 Angle : 0.551 5.520 3196 Z= 0.283 Chirality : 0.041 0.190 383 Planarity : 0.006 0.074 375 Dihedral : 4.928 41.857 315 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % 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: 2.13 (0.52), residues: 277 helix: 2.70 (0.35), residues: 204 sheet: None (None), residues: 0 loop : -2.64 (0.68), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 441 HIS 0.001 0.000 HIS R 30 PHE 0.015 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 0.04405 ( 160) hydrogen bonds : angle 3.76692 ( 480) SS BOND : bond 0.00686 ( 1) SS BOND : angle 2.43949 ( 2) covalent geometry : bond 0.00315 ( 2331) covalent geometry : angle 0.54734 ( 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 : 0.270 Fit side-chains REVERT: R 457 MET cc_start: 0.8914 (mtp) cc_final: 0.8711 (mtp) outliers start: 6 outliers final: 5 residues processed: 33 average time/residue: 0.1362 time to fit residues: 5.4932 Evaluate side-chains 32 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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: 7.9990 chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 25 optimal weight: 0.0060 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 6 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 = 0.3466 r_free = 0.3466 target = 0.094399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.078257 restraints weight = 5076.526| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.83 r_work: 0.3090 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 2332 Z= 0.114 Angle : 0.530 5.929 3196 Z= 0.269 Chirality : 0.041 0.198 383 Planarity : 0.005 0.067 375 Dihedral : 3.646 23.477 313 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.69 % Allowed : 22.13 % Favored : 74.18 % 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: 2.31 (0.52), residues: 277 helix: 2.82 (0.35), residues: 204 sheet: None (None), residues: 0 loop : -2.53 (0.67), residues: 73 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 0.012 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 0.03846 ( 160) hydrogen bonds : angle 3.62530 ( 480) SS BOND : bond 0.00360 ( 1) SS BOND : angle 1.97293 ( 2) covalent geometry : bond 0.00247 ( 2331) covalent geometry : angle 0.52811 ( 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 38 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.262 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 35 average time/residue: 0.1352 time to fit residues: 5.8763 Evaluate side-chains 32 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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: 1.9990 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 24 optimal weight: 0.0570 chunk 1 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- 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 = 0.3450 r_free = 0.3450 target = 0.093396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.077435 restraints weight = 5094.765| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.84 r_work: 0.3079 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1086 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= 0.113 Angle : 0.548 8.944 3196 Z= 0.270 Chirality : 0.041 0.198 383 Planarity : 0.005 0.063 375 Dihedral : 3.602 23.143 313 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.87 % Allowed : 23.77 % 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: 2.47 (0.52), residues: 277 helix: 2.94 (0.35), residues: 204 sheet: None (None), residues: 0 loop : -2.50 (0.67), residues: 73 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 0.010 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 0.03759 ( 160) hydrogen bonds : angle 3.58629 ( 480) SS BOND : bond 0.00206 ( 1) SS BOND : angle 1.77240 ( 2) covalent geometry : bond 0.00252 ( 2331) covalent geometry : angle 0.54681 ( 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 37 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.263 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 36 average time/residue: 0.1357 time to fit residues: 5.9508 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 : 0.257 ------------------------------------------------------------------------------- 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 200 PHE Chi-restraints excluded: chain R residue 412 LEU 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: 1.9990 chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 0.0870 chunk 27 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 overall best weight: 1.2166 ------------------------------------------------------------------------------- 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 = 0.3423 r_free = 0.3423 target = 0.091555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.075798 restraints weight = 5206.668| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.82 r_work: 0.3046 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2332 Z= 0.125 Angle : 0.557 9.811 3196 Z= 0.273 Chirality : 0.042 0.197 383 Planarity : 0.005 0.062 375 Dihedral : 3.597 23.230 313 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.87 % Allowed : 24.18 % Favored : 72.95 % 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: 2.51 (0.52), residues: 277 helix: 2.97 (0.35), residues: 206 sheet: None (None), residues: 0 loop : -2.62 (0.68), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 170 HIS 0.002 0.000 HIS R 135 PHE 0.008 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 0.04060 ( 160) hydrogen bonds : angle 3.58883 ( 480) SS BOND : bond 0.00458 ( 1) SS BOND : angle 1.75484 ( 2) covalent geometry : bond 0.00299 ( 2331) covalent geometry : angle 0.55570 ( 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 36 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.265 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 35 average time/residue: 0.1399 time to fit residues: 6.0415 Evaluate side-chains 31 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 0.5980 chunk 4 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 13 optimal weight: 0.0570 chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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 = 0.3452 r_free = 0.3452 target = 0.093439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.077542 restraints weight = 5102.336| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.81 r_work: 0.3079 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2332 Z= 0.111 Angle : 0.539 9.524 3196 Z= 0.264 Chirality : 0.041 0.202 383 Planarity : 0.005 0.061 375 Dihedral : 3.542 22.275 313 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.64 % Allowed : 27.05 % 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: 2.55 (0.52), residues: 277 helix: 3.02 (0.35), residues: 206 sheet: None (None), residues: 0 loop : -2.69 (0.67), 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 0.008 0.001 PHE R 200 TYR 0.009 0.001 TYR R 454 ARG 0.002 0.000 ARG R 221 Details of bonding type rmsd hydrogen bonds : bond 0.03618 ( 160) hydrogen bonds : angle 3.52380 ( 480) SS BOND : bond 0.00074 ( 1) SS BOND : angle 1.64477 ( 2) covalent geometry : bond 0.00252 ( 2331) covalent geometry : angle 0.53743 ( 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 33 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.273 Fit side-chains REVERT: R 77 ASP cc_start: 0.8483 (t70) cc_final: 0.8280 (t70) outliers start: 4 outliers final: 1 residues processed: 32 average time/residue: 0.1453 time to fit residues: 5.7196 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 : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3444 r_free = 0.3444 target = 0.092932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.076975 restraints weight = 5205.136| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.84 r_work: 0.3069 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2332 Z= 0.113 Angle : 0.545 9.512 3196 Z= 0.265 Chirality : 0.041 0.203 383 Planarity : 0.005 0.061 375 Dihedral : 3.516 22.341 313 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % 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: 2.58 (0.52), residues: 277 helix: 3.05 (0.35), residues: 206 sheet: None (None), residues: 0 loop : -2.73 (0.67), residues: 71 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 0.007 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 0.03699 ( 160) hydrogen bonds : angle 3.51586 ( 480) SS BOND : bond 0.00123 ( 1) SS BOND : angle 1.56306 ( 2) covalent geometry : bond 0.00263 ( 2331) covalent geometry : angle 0.54376 ( 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 35 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.268 Fit side-chains REVERT: R 77 ASP cc_start: 0.8504 (t70) cc_final: 0.8303 (t70) REVERT: R 464 GLU cc_start: 0.8844 (tp30) cc_final: 0.8624 (tp30) outliers start: 4 outliers final: 1 residues processed: 35 average time/residue: 0.1353 time to fit residues: 5.8548 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 : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 19 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 24 optimal weight: 0.0870 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: 1.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- 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 = 0.3448 r_free = 0.3448 target = 0.093313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.077311 restraints weight = 5278.812| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.87 r_work: 0.3080 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1468 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= 0.112 Angle : 0.548 9.408 3196 Z= 0.267 Chirality : 0.042 0.214 383 Planarity : 0.005 0.059 375 Dihedral : 3.537 22.135 313 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % 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: 2.61 (0.52), residues: 277 helix: 3.06 (0.35), residues: 206 sheet: None (None), residues: 0 loop : -2.69 (0.67), residues: 71 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 0.03567 ( 160) hydrogen bonds : angle 3.50869 ( 480) SS BOND : bond 0.00226 ( 1) SS BOND : angle 1.68749 ( 2) covalent geometry : bond 0.00259 ( 2331) covalent geometry : angle 0.54647 ( 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 35 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.272 Fit side-chains REVERT: R 77 ASP cc_start: 0.8520 (t70) cc_final: 0.8309 (t70) REVERT: R 464 GLU cc_start: 0.8828 (tp30) cc_final: 0.8592 (tp30) outliers start: 5 outliers final: 1 residues processed: 35 average time/residue: 0.1335 time to fit residues: 5.8242 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 : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 25 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3424 r_free = 0.3424 target = 0.091762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.075751 restraints weight = 5192.949| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.80 r_work: 0.3053 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1546 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= 0.122 Angle : 0.560 9.075 3196 Z= 0.273 Chirality : 0.042 0.214 383 Planarity : 0.005 0.060 375 Dihedral : 3.575 22.704 313 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.15 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: 2.60 (0.52), residues: 277 helix: 3.06 (0.35), residues: 206 sheet: None (None), residues: 0 loop : -2.71 (0.67), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 170 HIS 0.002 0.000 HIS R 135 PHE 0.009 0.001 PHE R 200 TYR 0.011 0.001 TYR R 454 ARG 0.001 0.000 ARG R 178 Details of bonding type rmsd hydrogen bonds : bond 0.03899 ( 160) hydrogen bonds : angle 3.54869 ( 480) SS BOND : bond 0.00026 ( 1) SS BOND : angle 1.99765 ( 2) covalent geometry : bond 0.00293 ( 2331) covalent geometry : angle 0.55752 ( 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 31 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.266 Fit side-chains REVERT: R 464 GLU cc_start: 0.8860 (tp30) cc_final: 0.8611 (tp30) outliers start: 2 outliers final: 1 residues processed: 31 average time/residue: 0.1392 time to fit residues: 5.2564 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 : 0.219 ------------------------------------------------------------------------------- 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: 0.7980 chunk 11 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 17 optimal weight: 0.3980 chunk 8 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3452 r_free = 0.3452 target = 0.093424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.077376 restraints weight = 5165.082| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.84 r_work: 0.3077 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1565 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= 0.112 Angle : 0.549 9.035 3196 Z= 0.267 Chirality : 0.042 0.219 383 Planarity : 0.005 0.059 375 Dihedral : 3.569 22.251 313 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.41 % Allowed : 29.10 % Favored : 70.49 % 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: 2.63 (0.52), residues: 277 helix: 3.08 (0.35), residues: 206 sheet: None (None), residues: 0 loop : -2.70 (0.67), residues: 71 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 0.010 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 0.03513 ( 160) hydrogen bonds : angle 3.49893 ( 480) SS BOND : bond 0.00145 ( 1) SS BOND : angle 1.84860 ( 2) covalent geometry : bond 0.00256 ( 2331) covalent geometry : angle 0.54687 ( 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: 1 poor density : 32 time to evaluate : 0.255 Fit side-chains REVERT: R 77 ASP cc_start: 0.8452 (t70) cc_final: 0.8140 (t70) REVERT: R 464 GLU cc_start: 0.8826 (tp30) cc_final: 0.8585 (tp30) outliers start: 1 outliers final: 1 residues processed: 33 average time/residue: 0.1422 time to fit residues: 5.8017 Evaluate side-chains 31 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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: 5.9990 chunk 2 optimal weight: 3.9990 chunk 14 optimal weight: 0.0000 chunk 22 optimal weight: 0.0970 chunk 11 optimal weight: 0.0570 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 overall best weight: 0.4302 ------------------------------------------------------------------------------- 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 = 0.3450 r_free = 0.3450 target = 0.093549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.077234 restraints weight = 5115.150| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.90 r_work: 0.3078 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 2332 Z= 0.110 Angle : 0.516 5.819 3196 Z= 0.258 Chirality : 0.041 0.218 383 Planarity : 0.005 0.057 375 Dihedral : 3.564 21.987 313 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.82 % Allowed : 28.69 % Favored : 70.49 % 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: 2.65 (0.52), residues: 277 helix: 3.10 (0.34), residues: 206 sheet: None (None), residues: 0 loop : -2.67 (0.67), residues: 71 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 0.010 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 0.03402 ( 160) hydrogen bonds : angle 3.47188 ( 480) SS BOND : bond 0.00052 ( 1) SS BOND : angle 1.49658 ( 2) covalent geometry : bond 0.00245 ( 2331) covalent geometry : angle 0.51457 ( 3194) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1423.84 seconds wall clock time: 25 minutes 8.32 seconds (1508.32 seconds total)