Starting phenix.real_space_refine on Tue Aug 4 11:46:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v3y_64761/08_2026/9v3y_64761.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v3y_64761/08_2026/9v3y_64761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v3y_64761/08_2026/9v3y_64761.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v3y_64761/08_2026/9v3y_64761.map" model { file = "/net/cci-nas-00/data/ceres_data/9v3y_64761/08_2026/9v3y_64761.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v3y_64761/08_2026/9v3y_64761.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 1295 2.51 5 N 336 2.21 5 O 310 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 1956 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 50 Classifications: {'peptide': 5} Link IDs: {'PTRANS': 1, 'TRANS': 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MEA:plan-2': 1, 'ZAL:plan-1': 1, 'ALC:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Classifications: {'peptide': 1} Modifications used: {'COO': 1, 'PEPT-D': 1} Chain: "R" Number of atoms: 1894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1894 Classifications: {'peptide': 254} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 237} Chain breaks: 1 Time building chain proxies: 1.36, per 1000 atoms: 0.70 Number of scatterers: 1956 At special positions: 0 Unit cell: (49.8015, 55.335, 83.0025, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 310 8.00 N 336 7.00 C 1295 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 107 " - pdb=" SG CYS R 186 " distance=2.03 Simple disulfide: pdb=" SG CYS R 133 " - pdb=" SG CYS R 219 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.33 Conformation dependent library (CDL) restraints added in 82.7 milliseconds 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB ZAL C 4 " Input residue name is d-peptide pdb=" CB DAR C 6 " Number of C-beta restraints generated: 478 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 1 sheets defined 84.2% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'R' and resid 38 through 64 Proline residue: R 51 - end of helix Processing helix chain 'R' and resid 65 through 66 No H-bonds generated for 'chain 'R' and resid 65 through 66' Processing helix chain 'R' and resid 67 through 68 No H-bonds generated for 'chain 'R' and resid 67 through 68' Processing helix chain 'R' and resid 69 through 85 removed outlier: 3.990A pdb=" N LEU R 73 " --> pdb=" O GLY R 69 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 96 removed outlier: 3.694A pdb=" N VAL R 92 " --> pdb=" O PRO R 88 " (cutoff:3.500A) Proline residue: R 93 - end of helix Processing helix chain 'R' and resid 102 through 137 Proline residue: R 111 - end of helix Processing helix chain 'R' and resid 143 through 172 removed outlier: 4.183A pdb=" N GLN R 152 " --> pdb=" O ALA R 148 " (cutoff:3.500A) Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 195 through 209 Processing helix chain 'R' and resid 209 through 225 Processing helix chain 'R' and resid 231 through 259 Proline residue: R 248 - end of helix Processing helix chain 'R' and resid 263 through 294 Proline residue: R 274 - end of helix removed outlier: 4.357A pdb=" N SER R 284 " --> pdb=" O ALA R 280 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N CYS R 285 " --> pdb=" O LEU R 281 " (cutoff:3.500A) Proline residue: R 288 - end of helix Processing sheet with id=AA1, first strand: chain 'C' and resid 2 through 3 160 hydrogen bonds defined for protein. 471 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.39 Time building geometry restraints manager: 0.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 603 1.34 - 1.46: 379 1.46 - 1.58: 1010 1.58 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 2010 Sorted by residual: bond pdb=" CA ZAL C 4 " pdb=" C ZAL C 4 " ideal model delta sigma weight residual 1.525 1.567 -0.042 2.10e-02 2.27e+03 3.98e+00 bond pdb=" C ZAL C 4 " pdb=" O ZAL C 4 " ideal model delta sigma weight residual 1.231 1.264 -0.033 2.00e-02 2.50e+03 2.74e+00 bond pdb=" CB THR R 117 " pdb=" CG2 THR R 117 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.26e+00 bond pdb=" CG PRO R 181 " pdb=" CD PRO R 181 " ideal model delta sigma weight residual 1.512 1.491 0.021 2.70e-02 1.37e+03 6.04e-01 bond pdb=" CA ALA R 37 " pdb=" C ALA R 37 " ideal model delta sigma weight residual 1.525 1.541 -0.016 2.10e-02 2.27e+03 5.99e-01 ... (remaining 2005 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 2602 1.03 - 2.06: 108 2.06 - 3.10: 27 3.10 - 4.13: 3 4.13 - 5.16: 12 Bond angle restraints: 2752 Sorted by residual: angle pdb=" N ALC C 5 " pdb=" CA ALC C 5 " pdb=" CB ALC C 5 " ideal model delta sigma weight residual 110.40 115.00 -4.60 1.50e+00 4.44e-01 9.41e+00 angle pdb=" N VAL R 167 " pdb=" CA VAL R 167 " pdb=" C VAL R 167 " ideal model delta sigma weight residual 108.88 113.47 -4.59 2.16e+00 2.14e-01 4.52e+00 angle pdb=" CA ARG R 147 " pdb=" CB ARG R 147 " pdb=" CG ARG R 147 " ideal model delta sigma weight residual 114.10 118.21 -4.11 2.00e+00 2.50e-01 4.23e+00 angle pdb=" C GLY R 150 " pdb=" N VAL R 151 " pdb=" CA VAL R 151 " ideal model delta sigma weight residual 120.56 118.20 2.36 1.26e+00 6.30e-01 3.52e+00 angle pdb=" CA VAL R 167 " pdb=" C VAL R 167 " pdb=" N PRO R 168 " ideal model delta sigma weight residual 118.88 121.56 -2.68 1.54e+00 4.22e-01 3.03e+00 ... (remaining 2747 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.07: 1118 23.07 - 46.13: 40 46.13 - 69.20: 2 69.20 - 92.27: 3 92.27 - 115.34: 2 Dihedral angle restraints: 1165 sinusoidal: 424 harmonic: 741 Sorted by residual: dihedral pdb=" CB CYS R 133 " pdb=" SG CYS R 133 " pdb=" SG CYS R 219 " pdb=" CB CYS R 219 " ideal model delta sinusoidal sigma weight residual 93.00 6.61 86.39 1 1.00e+01 1.00e-02 9.00e+01 dihedral pdb=" CD1 ALC C 5 " pdb=" CE1 ALC C 5 " pdb=" CZ ALC C 5 " pdb=" CE2 ALC C 5 " ideal model delta sinusoidal sigma weight residual 55.37 -59.97 115.34 1 3.00e+01 1.11e-03 1.52e+01 dihedral pdb=" CG ALC C 5 " pdb=" CD1 ALC C 5 " pdb=" CE1 ALC C 5 " pdb=" CZ ALC C 5 " ideal model delta sinusoidal sigma weight residual -55.84 51.62 -107.46 1 3.00e+01 1.11e-03 1.39e+01 ... (remaining 1162 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.010: 331 1.010 - 2.020: 0 2.020 - 3.030: 0 3.030 - 4.040: 0 4.040 - 5.049: 1 Chirality restraints: 332 Sorted by residual: chirality pdb=" CG ALC C 5 " pdb=" CB ALC C 5 " pdb=" CD1 ALC C 5 " pdb=" CD2 ALC C 5 " both_signs ideal model delta sigma weight residual False -2.52 2.53 -5.05 2.00e-01 2.50e+01 6.37e+02 chirality pdb=" CA TRP R 246 " pdb=" N TRP R 246 " pdb=" C TRP R 246 " pdb=" CB TRP R 246 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 3.95e-01 chirality pdb=" CA HIS R 179 " pdb=" N HIS R 179 " pdb=" C HIS R 179 " pdb=" CB HIS R 179 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.22e-01 ... (remaining 329 not shown) Planarity restraints: 335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY R 211 " -0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO R 212 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO R 212 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO R 212 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP R 100 " 0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO R 101 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO R 101 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO R 101 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL R 167 " -0.021 5.00e-02 4.00e+02 3.13e-02 1.57e+00 pdb=" N PRO R 168 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO R 168 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 168 " -0.018 5.00e-02 4.00e+02 ... (remaining 332 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 482 2.81 - 3.33: 1954 3.33 - 3.85: 3349 3.85 - 4.38: 3363 4.38 - 4.90: 6370 Nonbonded interactions: 15518 Sorted by model distance: nonbonded pdb=" O ZAL C 4 " pdb=" NH1 ARG R 173 " model vdw 2.287 3.120 nonbonded pdb=" OD2 ASP R 131 " pdb=" NH1 ARG R 147 " model vdw 2.321 3.120 nonbonded pdb=" O SER R 218 " pdb=" OG SER R 221 " model vdw 2.501 3.040 nonbonded pdb=" OE2 GLU R 178 " pdb=" NE2 GLN R 185 " model vdw 2.517 3.120 nonbonded pdb=" O SER R 194 " pdb=" OG SER R 194 " model vdw 2.544 3.040 ... (remaining 15513 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 3.170 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: 0.020 Extract box with map and model: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.180 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:2.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 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 : 0.004 0.103 2013 Z= 0.274 Angle : 0.582 5.162 2756 Z= 0.291 Chirality : 0.280 5.049 332 Planarity : 0.005 0.035 335 Dihedral : 13.600 115.336 681 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.11 (0.56), residues: 250 helix: 2.88 (0.36), residues: 206 sheet: -3.31 (1.23), residues: 12 loop : -1.56 (1.09), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 147 TYR 0.006 0.001 TYR R 172 PHE 0.008 0.001 PHE R 46 TRP 0.009 0.001 TRP R 246 HIS 0.002 0.001 HIS R 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 2010) covalent geometry : angle 0.58002 / 0.29 ( 2752) SS BOND : bond 0.00462 / 0.23 ( 2) SS BOND : angle 1.40858 / 0.66 ( 4) hydrogen bonds : bond 0.10344 / 6.38 ( 160) hydrogen bonds : angle 5.08275 / 3.51 ( 471) Misc. bond : bond 0.10266 / 5.40 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.069 Fit side-chains REVERT: R 167 VAL cc_start: 0.7918 (t) cc_final: 0.7705 (m) REVERT: R 240 VAL cc_start: 0.7425 (t) cc_final: 0.7210 (m) REVERT: R 271 ARG cc_start: 0.7734 (mtt180) cc_final: 0.7414 (tpt170) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0859 time to fit residues: 3.5139 Evaluate side-chains 26 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 0.0670 chunk 18 optimal weight: 4.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.174226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.133536 restraints weight = 2429.253| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.07 r_work: 0.3456 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2013 Z= 0.147 Angle : 0.594 5.235 2756 Z= 0.287 Chirality : 0.039 0.135 332 Planarity : 0.006 0.038 335 Dihedral : 8.660 89.851 291 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.54 % Allowed : 7.18 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.95 (0.55), residues: 250 helix: 2.78 (0.36), residues: 206 sheet: -3.64 (1.31), residues: 12 loop : -1.58 (1.06), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 173 TYR 0.005 0.001 TYR R 172 PHE 0.007 0.001 PHE R 46 TRP 0.008 0.001 TRP R 246 HIS 0.002 0.001 HIS R 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 2010) covalent geometry : angle 0.59129 / 0.29 ( 2752) SS BOND : bond 0.00613 / 0.31 ( 2) SS BOND : angle 1.54511 / 0.73 ( 4) hydrogen bonds : bond 0.03867 / 2.64 ( 160) hydrogen bonds : angle 4.61031 / 3.19 ( 471) Misc. bond : bond 0.00037 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.115 Fit side-chains REVERT: R 271 ARG cc_start: 0.7881 (mtt180) cc_final: 0.7436 (tpt170) outliers start: 3 outliers final: 1 residues processed: 27 average time/residue: 0.0723 time to fit residues: 2.3224 Evaluate side-chains 25 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 256 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 13 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 11 optimal weight: 0.0870 chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 176 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.174535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.134280 restraints weight = 2444.730| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.06 r_work: 0.3474 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2013 Z= 0.134 Angle : 0.571 5.168 2756 Z= 0.277 Chirality : 0.039 0.197 332 Planarity : 0.005 0.038 335 Dihedral : 8.487 81.504 291 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.54 % Allowed : 8.72 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.98 (0.56), residues: 250 helix: 2.78 (0.36), residues: 206 sheet: -3.66 (1.29), residues: 12 loop : -1.42 (1.06), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 96 TYR 0.005 0.001 TYR R 172 PHE 0.007 0.001 PHE R 46 TRP 0.007 0.001 TRP R 246 HIS 0.002 0.001 HIS R 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 2010) covalent geometry : angle 0.56922 / 0.28 ( 2752) SS BOND : bond 0.00535 / 0.27 ( 2) SS BOND : angle 1.33926 / 0.62 ( 4) hydrogen bonds : bond 0.03705 / 2.56 ( 160) hydrogen bonds : angle 4.53273 / 3.14 ( 471) Misc. bond : bond 0.00007 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.051 Fit side-chains REVERT: R 271 ARG cc_start: 0.7889 (mtt180) cc_final: 0.7440 (tpt170) outliers start: 3 outliers final: 2 residues processed: 25 average time/residue: 0.0708 time to fit residues: 2.0492 Evaluate side-chains 25 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 256 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 3 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 2 optimal weight: 0.0370 chunk 17 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.171558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.131271 restraints weight = 2438.762| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.03 r_work: 0.3442 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 2013 Z= 0.165 Angle : 0.603 5.236 2756 Z= 0.292 Chirality : 0.041 0.148 332 Planarity : 0.005 0.041 335 Dihedral : 8.399 77.248 291 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.56 % Allowed : 9.23 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.77 (0.54), residues: 250 helix: 2.60 (0.36), residues: 206 sheet: -3.00 (1.41), residues: 10 loop : -1.68 (1.00), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 96 TYR 0.010 0.001 TYR R 172 PHE 0.008 0.001 PHE R 46 TRP 0.010 0.001 TRP R 246 HIS 0.002 0.001 HIS R 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.16 ( 2010) covalent geometry : angle 0.60032 / 0.29 ( 2752) SS BOND : bond 0.00577 / 0.29 ( 2) SS BOND : angle 1.51164 / 0.69 ( 4) hydrogen bonds : bond 0.04008 / 2.77 ( 160) hydrogen bonds : angle 4.66543 / 3.23 ( 471) Misc. bond : bond 0.00003 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.076 Fit side-chains REVERT: R 271 ARG cc_start: 0.7987 (mtt180) cc_final: 0.7478 (tpt170) outliers start: 5 outliers final: 3 residues processed: 25 average time/residue: 0.0728 time to fit residues: 2.1523 Evaluate side-chains 25 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 256 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 11 optimal weight: 0.0470 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.172723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.131722 restraints weight = 2397.141| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.06 r_work: 0.3443 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 2013 Z= 0.144 Angle : 0.576 5.115 2756 Z= 0.282 Chirality : 0.039 0.127 332 Planarity : 0.005 0.040 335 Dihedral : 8.198 81.307 291 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.59 % Allowed : 9.74 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.88 (0.55), residues: 250 helix: 2.66 (0.36), residues: 206 sheet: -2.93 (1.40), residues: 10 loop : -1.51 (1.00), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 96 TYR 0.007 0.001 TYR R 172 PHE 0.007 0.001 PHE R 46 TRP 0.009 0.001 TRP R 246 HIS 0.002 0.001 HIS R 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 ( 2010) covalent geometry : angle 0.57422 / 0.28 ( 2752) SS BOND : bond 0.00541 / 0.27 ( 2) SS BOND : angle 1.38775 / 0.63 ( 4) hydrogen bonds : bond 0.03852 / 2.67 ( 160) hydrogen bonds : angle 4.60614 / 3.19 ( 471) Misc. bond : bond 0.00016 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.067 Fit side-chains REVERT: R 65 ARG cc_start: 0.5901 (mmt180) cc_final: 0.5537 (mmt90) REVERT: R 271 ARG cc_start: 0.7968 (mtt180) cc_final: 0.7473 (tpt170) outliers start: 7 outliers final: 6 residues processed: 26 average time/residue: 0.0694 time to fit residues: 2.1153 Evaluate side-chains 25 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 286 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 0.0970 chunk 3 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 6 optimal weight: 0.0050 chunk 19 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.173392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.132715 restraints weight = 2443.930| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.07 r_work: 0.3432 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2013 Z= 0.135 Angle : 0.571 5.120 2756 Z= 0.275 Chirality : 0.038 0.122 332 Planarity : 0.005 0.040 335 Dihedral : 8.009 82.945 291 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.59 % Allowed : 10.77 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.89 (0.54), residues: 250 helix: 2.68 (0.35), residues: 206 sheet: -3.53 (1.25), residues: 12 loop : -1.14 (1.05), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 96 TYR 0.007 0.001 TYR R 172 PHE 0.007 0.001 PHE R 46 TRP 0.007 0.001 TRP R 246 HIS 0.002 0.001 HIS R 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 2010) covalent geometry : angle 0.56887 / 0.27 ( 2752) SS BOND : bond 0.00514 / 0.26 ( 2) SS BOND : angle 1.28733 / 0.58 ( 4) hydrogen bonds : bond 0.03698 / 2.56 ( 160) hydrogen bonds : angle 4.50186 / 3.13 ( 471) Misc. bond : bond 0.00024 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 0.042 Fit side-chains REVERT: R 65 ARG cc_start: 0.5902 (mmt180) cc_final: 0.5551 (mmt90) REVERT: R 271 ARG cc_start: 0.7974 (mtt180) cc_final: 0.7493 (tpt170) outliers start: 7 outliers final: 6 residues processed: 25 average time/residue: 0.0669 time to fit residues: 1.9798 Evaluate side-chains 25 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 286 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 10 optimal weight: 0.6980 chunk 7 optimal weight: 0.0170 chunk 8 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 5 optimal weight: 0.2980 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 6 optimal weight: 0.3980 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.178534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.139777 restraints weight = 2452.787| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 1.88 r_work: 0.3573 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 2013 Z= 0.129 Angle : 0.572 6.518 2756 Z= 0.276 Chirality : 0.038 0.122 332 Planarity : 0.005 0.040 335 Dihedral : 7.804 82.985 291 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.05 % Allowed : 13.33 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.07 (0.54), residues: 250 helix: 2.78 (0.35), residues: 206 sheet: -3.41 (1.32), residues: 12 loop : -1.00 (1.05), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 96 TYR 0.006 0.001 TYR R 172 PHE 0.007 0.001 PHE R 46 TRP 0.007 0.001 TRP R 72 HIS 0.002 0.001 HIS R 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 2010) covalent geometry : angle 0.57007 / 0.28 ( 2752) SS BOND : bond 0.00504 / 0.25 ( 2) SS BOND : angle 1.21803 / 0.55 ( 4) hydrogen bonds : bond 0.03611 / 2.50 ( 160) hydrogen bonds : angle 4.54458 / 3.14 ( 471) Misc. bond : bond 0.00041 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.068 Fit side-chains REVERT: R 65 ARG cc_start: 0.6046 (mmt180) cc_final: 0.5710 (mmt90) REVERT: R 271 ARG cc_start: 0.7971 (mtt180) cc_final: 0.7544 (tpt170) outliers start: 4 outliers final: 3 residues processed: 22 average time/residue: 0.0816 time to fit residues: 2.0881 Evaluate side-chains 22 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 286 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 16 optimal weight: 0.0170 chunk 5 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 6 optimal weight: 0.0010 chunk 22 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 0.0770 overall best weight: 0.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.179964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.141404 restraints weight = 2460.601| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.89 r_work: 0.3590 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 2013 Z= 0.123 Angle : 0.557 5.150 2756 Z= 0.268 Chirality : 0.037 0.122 332 Planarity : 0.005 0.039 335 Dihedral : 7.601 83.654 291 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.56 % Allowed : 12.82 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.28 (0.54), residues: 250 helix: 2.93 (0.35), residues: 206 sheet: -3.40 (1.32), residues: 12 loop : -0.87 (1.05), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 96 TYR 0.005 0.001 TYR R 190 PHE 0.007 0.001 PHE R 46 TRP 0.008 0.001 TRP R 246 HIS 0.002 0.001 HIS R 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 2010) covalent geometry : angle 0.55589 / 0.27 ( 2752) SS BOND : bond 0.00493 / 0.25 ( 2) SS BOND : angle 1.19386 / 0.54 ( 4) hydrogen bonds : bond 0.03423 / 2.36 ( 160) hydrogen bonds : angle 4.40386 / 3.06 ( 471) Misc. bond : bond 0.00032 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 19 time to evaluate : 0.072 Fit side-chains REVERT: R 271 ARG cc_start: 0.7971 (mtt180) cc_final: 0.7535 (tpt170) outliers start: 5 outliers final: 3 residues processed: 22 average time/residue: 0.1018 time to fit residues: 2.5460 Evaluate side-chains 22 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 286 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 9 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 0 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.176061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.140798 restraints weight = 2388.000| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 1.98 r_work: 0.3532 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 2013 Z= 0.153 Angle : 0.594 5.665 2756 Z= 0.285 Chirality : 0.039 0.133 332 Planarity : 0.005 0.040 335 Dihedral : 7.643 85.724 291 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.05 % Allowed : 11.79 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.03 (0.53), residues: 250 helix: 2.72 (0.35), residues: 207 sheet: -3.50 (1.25), residues: 12 loop : -0.80 (1.07), residues: 31 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 147 TYR 0.008 0.001 TYR R 172 PHE 0.008 0.001 PHE R 46 TRP 0.009 0.001 TRP R 246 HIS 0.002 0.001 HIS R 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 ( 2010) covalent geometry : angle 0.59197 / 0.28 ( 2752) SS BOND : bond 0.00523 / 0.26 ( 2) SS BOND : angle 1.32168 / 0.60 ( 4) hydrogen bonds : bond 0.03777 / 2.63 ( 160) hydrogen bonds : angle 4.55290 / 3.17 ( 471) Misc. bond : bond 0.00047 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.070 Fit side-chains REVERT: R 271 ARG cc_start: 0.7980 (mtt180) cc_final: 0.7547 (tpt170) outliers start: 4 outliers final: 4 residues processed: 23 average time/residue: 0.0778 time to fit residues: 2.0744 Evaluate side-chains 24 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 131 ASP Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 286 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 8 optimal weight: 0.0030 chunk 11 optimal weight: 0.0020 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 0 optimal weight: 0.6980 chunk 19 optimal weight: 0.1980 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.180898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.141705 restraints weight = 2503.745| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.91 r_work: 0.3589 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2013 Z= 0.124 Angle : 0.570 5.350 2756 Z= 0.272 Chirality : 0.040 0.246 332 Planarity : 0.005 0.038 335 Dihedral : 7.524 86.114 291 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.05 % Allowed : 12.82 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.19 (0.53), residues: 250 helix: 2.81 (0.35), residues: 207 sheet: -3.30 (1.33), residues: 12 loop : -0.66 (1.07), residues: 31 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 147 TYR 0.005 0.001 TYR R 190 PHE 0.006 0.001 PHE R 46 TRP 0.008 0.001 TRP R 72 HIS 0.002 0.001 HIS R 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 2010) covalent geometry : angle 0.56946 / 0.27 ( 2752) SS BOND : bond 0.00506 / 0.26 ( 2) SS BOND : angle 1.03982 / 0.43 ( 4) hydrogen bonds : bond 0.03553 / 2.47 ( 160) hydrogen bonds : angle 4.40885 / 3.10 ( 471) Misc. bond : bond 0.00040 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.083 Fit side-chains REVERT: R 271 ARG cc_start: 0.7992 (mtt180) cc_final: 0.7533 (tpt170) outliers start: 4 outliers final: 3 residues processed: 21 average time/residue: 0.0634 time to fit residues: 1.5638 Evaluate side-chains 23 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 286 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 6 optimal weight: 0.0470 chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 0.0010 chunk 9 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 overall best weight: 0.4484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.180048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.140736 restraints weight = 2512.892| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 1.91 r_work: 0.3576 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2013 Z= 0.130 Angle : 0.574 5.150 2756 Z= 0.275 Chirality : 0.040 0.232 332 Planarity : 0.005 0.039 335 Dihedral : 7.488 87.099 291 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.05 % Allowed : 12.31 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.17 (0.53), residues: 250 helix: 2.80 (0.35), residues: 207 sheet: -3.33 (1.30), residues: 12 loop : -0.70 (1.07), residues: 31 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 147 TYR 0.007 0.001 TYR R 172 PHE 0.007 0.001 PHE R 46 TRP 0.009 0.001 TRP R 246 HIS 0.002 0.001 HIS R 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 2010) covalent geometry : angle 0.57307 / 0.27 ( 2752) SS BOND : bond 0.00491 / 0.25 ( 2) SS BOND : angle 1.06231 / 0.45 ( 4) hydrogen bonds : bond 0.03594 / 2.50 ( 160) hydrogen bonds : angle 4.45249 / 3.13 ( 471) Misc. bond : bond 0.00043 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 798.08 seconds wall clock time: 14 minutes 20.15 seconds (860.15 seconds total)