Starting phenix.real_space_refine on Wed Sep 17 03:00:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z66_39793/09_2025/8z66_39793.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z66_39793/09_2025/8z66_39793.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 { model { file = "/net/cci-nas-00/data/ceres_data/8z66_39793/09_2025/8z66_39793.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z66_39793/09_2025/8z66_39793.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z66_39793/09_2025/8z66_39793.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z66_39793/09_2025/8z66_39793.map" } 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= 0.010 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 13 5.16 5 C 1468 2.51 5 N 377 2.21 5 O 362 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2220 Number of models: 1 Model: "" Number of chains: 1 Chain: "R" Number of atoms: 2220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2220 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 8, 'PHE:plan': 2, 'GLU:plan': 5, 'ASP:plan': 5, 'ASN:plan1': 3, 'TYR:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 119 Time building chain proxies: 0.91, per 1000 atoms: 0.41 Number of scatterers: 2220 At special positions: 0 Unit cell: (60.68, 71.34, 70.52, 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 13 16.00 O 362 8.00 N 377 7.00 C 1468 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 168 " distance=2.03 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: 0.19 Conformation dependent library (CDL) restraints added in 91.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 562 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 0 sheets defined 80.7% alpha, 0.0% 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 13 through 48 removed outlier: 3.966A pdb=" N HIS R 17 " --> pdb=" O SER R 13 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU R 18 " --> pdb=" O ARG R 14 " (cutoff:3.500A) Proline residue: R 20 - end of helix Proline residue: R 33 - end of helix Processing helix chain 'R' and resid 52 through 78 removed outlier: 3.686A pdb=" N TYR R 66 " --> pdb=" O ALA R 62 " (cutoff:3.500A) Proline residue: R 71 - end of helix Processing helix chain 'R' and resid 86 through 120 removed outlier: 4.582A pdb=" N ILE R 101 " --> pdb=" O PHE R 97 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N TYR R 102 " --> pdb=" O TYR R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 129 Processing helix chain 'R' and resid 130 through 149 Processing helix chain 'R' and resid 151 through 155 Processing helix chain 'R' and resid 177 through 190 removed outlier: 3.578A pdb=" N PHE R 190 " --> pdb=" O VAL R 186 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 210 removed outlier: 4.076A pdb=" N GLY R 210 " --> pdb=" O ARG R 206 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 252 Proline residue: R 239 - end of helix removed outlier: 3.552A pdb=" N LEU R 252 " --> pdb=" O SER R 248 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 276 Processing helix chain 'R' and resid 277 through 287 Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 290 through 304 removed outlier: 3.667A pdb=" N LEU R 304 " --> pdb=" O ALA R 300 " (cutoff:3.500A) 169 hydrogen bonds defined for protein. 498 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: 0.33 Time building geometry restraints manager: 0.27 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: 691 1.34 - 1.46: 620 1.46 - 1.58: 959 1.58 - 1.70: 0 1.70 - 1.82: 16 Bond restraints: 2286 Sorted by residual: bond pdb=" CB MET R 57 " pdb=" CG MET R 57 " ideal model delta sigma weight residual 1.520 1.451 0.069 3.00e-02 1.11e+03 5.32e+00 bond pdb=" CA MET R 57 " pdb=" C MET R 57 " ideal model delta sigma weight residual 1.523 1.500 0.023 1.34e-02 5.57e+03 3.01e+00 bond pdb=" SD MET R 57 " pdb=" CE MET R 57 " ideal model delta sigma weight residual 1.791 1.748 0.043 2.50e-02 1.60e+03 3.00e+00 bond pdb=" CB VAL R 54 " pdb=" CG2 VAL R 54 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.32e+00 bond pdb=" CB VAL R 141 " pdb=" CG1 VAL R 141 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.81e+00 ... (remaining 2281 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.81: 3113 3.81 - 7.63: 15 7.63 - 11.44: 1 11.44 - 15.25: 2 15.25 - 19.06: 1 Bond angle restraints: 3132 Sorted by residual: angle pdb=" C MET R 57 " pdb=" CA MET R 57 " pdb=" CB MET R 57 " ideal model delta sigma weight residual 110.42 91.36 19.06 1.99e+00 2.53e-01 9.18e+01 angle pdb=" N MET R 57 " pdb=" CA MET R 57 " pdb=" C MET R 57 " ideal model delta sigma weight residual 110.80 126.03 -15.23 2.13e+00 2.20e-01 5.11e+01 angle pdb=" CB MET R 57 " pdb=" CG MET R 57 " pdb=" SD MET R 57 " ideal model delta sigma weight residual 112.70 97.50 15.20 3.00e+00 1.11e-01 2.57e+01 angle pdb=" N GLY R 253 " pdb=" CA GLY R 253 " pdb=" C GLY R 253 " ideal model delta sigma weight residual 112.13 105.99 6.14 1.34e+00 5.57e-01 2.10e+01 angle pdb=" CA MET R 57 " pdb=" CB MET R 57 " pdb=" CG MET R 57 " ideal model delta sigma weight residual 114.10 121.50 -7.40 2.00e+00 2.50e-01 1.37e+01 ... (remaining 3127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.94: 1145 14.94 - 29.88: 115 29.88 - 44.83: 37 44.83 - 59.77: 4 59.77 - 74.71: 2 Dihedral angle restraints: 1303 sinusoidal: 434 harmonic: 869 Sorted by residual: dihedral pdb=" C MET R 57 " pdb=" N MET R 57 " pdb=" CA MET R 57 " pdb=" CB MET R 57 " ideal model delta harmonic sigma weight residual -122.60 -109.05 -13.55 0 2.50e+00 1.60e-01 2.94e+01 dihedral pdb=" CA THR R 166 " pdb=" C THR R 166 " pdb=" N PHE R 167 " pdb=" CA PHE R 167 " ideal model delta harmonic sigma weight residual -180.00 -159.09 -20.91 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CB CYS R 90 " pdb=" SG CYS R 90 " pdb=" SG CYS R 168 " pdb=" CB CYS R 168 " ideal model delta sinusoidal sigma weight residual 93.00 127.07 -34.07 1 1.00e+01 1.00e-02 1.65e+01 ... (remaining 1300 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 205 0.036 - 0.072: 115 0.072 - 0.109: 32 0.109 - 0.145: 9 0.145 - 0.181: 3 Chirality restraints: 364 Sorted by residual: chirality pdb=" CG LEU R 108 " pdb=" CB LEU R 108 " pdb=" CD1 LEU R 108 " pdb=" CD2 LEU R 108 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.17e-01 chirality pdb=" CG LEU R 272 " pdb=" CB LEU R 272 " pdb=" CD1 LEU R 272 " pdb=" CD2 LEU R 272 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.30e-01 chirality pdb=" CA LEU R 70 " pdb=" N LEU R 70 " pdb=" C LEU R 70 " pdb=" CB LEU R 70 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.53e-01 ... (remaining 361 not shown) Planarity restraints: 389 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE R 19 " -0.048 5.00e-02 4.00e+02 7.18e-02 8.26e+00 pdb=" N PRO R 20 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO R 20 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO R 20 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO R 20 " -0.044 5.00e-02 4.00e+02 6.59e-02 6.94e+00 pdb=" N PRO R 21 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO R 21 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO R 21 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 107 " -0.018 2.00e-02 2.50e+03 1.42e-02 3.55e+00 pdb=" CG PHE R 107 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE R 107 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE R 107 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE R 107 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE R 107 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE R 107 " -0.008 2.00e-02 2.50e+03 ... (remaining 386 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 473 2.77 - 3.31: 2238 3.31 - 3.84: 3713 3.84 - 4.37: 4131 4.37 - 4.90: 7228 Nonbonded interactions: 17783 Sorted by model distance: nonbonded pdb=" O ALA R 273 " pdb=" OG SER R 276 " model vdw 2.243 3.040 nonbonded pdb=" OH TYR R 43 " pdb=" NE2 GLN R 47 " model vdw 2.355 3.120 nonbonded pdb=" O MET R 57 " pdb=" CG1 ILE R 61 " model vdw 2.390 3.440 nonbonded pdb=" O LEU R 225 " pdb=" OG SER R 228 " model vdw 2.400 3.040 nonbonded pdb=" O ALA R 136 " pdb=" OG SER R 139 " model vdw 2.485 3.040 ... (remaining 17778 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: 2.820 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.870 Find NCS groups from input model: 0.000 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:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 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 : 0.006 0.069 2287 Z= 0.265 Angle : 0.942 19.064 3134 Z= 0.506 Chirality : 0.049 0.181 364 Planarity : 0.007 0.072 389 Dihedral : 13.496 74.712 738 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: -0.94 (0.47), residues: 292 helix: 0.46 (0.35), residues: 207 sheet: None (None), residues: 0 loop : -3.42 (0.51), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 202 TYR 0.023 0.002 TYR R 55 PHE 0.032 0.003 PHE R 107 TRP 0.014 0.002 TRP R 142 HIS 0.008 0.002 HIS R 17 Details of bonding type rmsd covalent geometry : bond 0.00626 ( 2286) covalent geometry : angle 0.94091 ( 3132) SS BOND : bond 0.00010 ( 1) SS BOND : angle 1.80582 ( 2) hydrogen bonds : bond 0.13951 ( 169) hydrogen bonds : angle 6.38803 ( 498) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.091 Fit side-chains REVERT: R 102 TYR cc_start: 0.8025 (m-80) cc_final: 0.7292 (m-80) REVERT: R 168 CYS cc_start: 0.5941 (t) cc_final: 0.5719 (t) REVERT: R 184 TYR cc_start: 0.7455 (t80) cc_final: 0.7226 (t80) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0971 time to fit residues: 4.8118 Evaluate side-chains 40 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 27 optimal weight: 0.9980 chunk 12 optimal weight: 0.2980 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 13 optimal weight: 0.0770 chunk 1 optimal weight: 0.0670 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 0.1980 chunk 15 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 26 optimal weight: 0.4980 overall best weight: 0.2276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.142707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.129274 restraints weight = 2975.954| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.36 r_work: 0.3556 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2287 Z= 0.173 Angle : 0.624 5.246 3134 Z= 0.330 Chirality : 0.042 0.137 364 Planarity : 0.006 0.049 389 Dihedral : 4.719 18.114 319 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.44 % Allowed : 10.53 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: 0.12 (0.49), residues: 292 helix: 1.26 (0.36), residues: 206 sheet: None (None), residues: 0 loop : -2.97 (0.60), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 130 TYR 0.016 0.002 TYR R 66 PHE 0.016 0.002 PHE R 265 TRP 0.008 0.001 TRP R 194 HIS 0.005 0.001 HIS R 302 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 2286) covalent geometry : angle 0.62372 ( 3132) SS BOND : bond 0.00048 ( 1) SS BOND : angle 0.84126 ( 2) hydrogen bonds : bond 0.04668 ( 169) hydrogen bonds : angle 4.78457 ( 498) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.085 Fit side-chains REVERT: R 83 TRP cc_start: 0.7369 (t-100) cc_final: 0.6958 (t-100) REVERT: R 102 TYR cc_start: 0.7929 (m-80) cc_final: 0.7353 (m-80) REVERT: R 168 CYS cc_start: 0.6200 (t) cc_final: 0.5960 (t) outliers start: 3 outliers final: 1 residues processed: 53 average time/residue: 0.0707 time to fit residues: 4.3671 Evaluate side-chains 45 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 196 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 12 optimal weight: 0.3980 chunk 27 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 4 optimal weight: 0.3980 chunk 7 optimal weight: 0.0670 chunk 9 optimal weight: 0.7980 chunk 6 optimal weight: 0.2980 chunk 23 optimal weight: 0.0570 chunk 15 optimal weight: 0.7980 chunk 21 optimal weight: 0.1980 chunk 28 optimal weight: 0.7980 overall best weight: 0.2036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.143159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.129592 restraints weight = 3067.413| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.38 r_work: 0.3558 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2287 Z= 0.149 Angle : 0.576 5.485 3134 Z= 0.304 Chirality : 0.042 0.141 364 Planarity : 0.005 0.049 389 Dihedral : 4.397 17.043 319 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.39 % Allowed : 14.83 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: 0.56 (0.50), residues: 292 helix: 1.61 (0.37), residues: 206 sheet: None (None), residues: 0 loop : -2.87 (0.59), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 130 TYR 0.015 0.001 TYR R 66 PHE 0.015 0.002 PHE R 237 TRP 0.007 0.001 TRP R 194 HIS 0.004 0.001 HIS R 302 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 2286) covalent geometry : angle 0.57622 ( 3132) SS BOND : bond 0.00033 ( 1) SS BOND : angle 0.79247 ( 2) hydrogen bonds : bond 0.04344 ( 169) hydrogen bonds : angle 4.59136 ( 498) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.079 Fit side-chains REVERT: R 102 TYR cc_start: 0.7954 (m-80) cc_final: 0.7331 (m-80) REVERT: R 169 PHE cc_start: 0.6165 (OUTLIER) cc_final: 0.5770 (m-10) REVERT: R 244 LEU cc_start: 0.7628 (tp) cc_final: 0.7392 (tp) outliers start: 5 outliers final: 2 residues processed: 50 average time/residue: 0.0542 time to fit residues: 3.3035 Evaluate side-chains 50 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 228 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 0.0170 chunk 20 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 0.0770 chunk 8 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 0.0980 chunk 17 optimal weight: 0.6980 overall best weight: 0.3176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.141890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.128933 restraints weight = 2965.078| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.31 r_work: 0.3553 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2287 Z= 0.187 Angle : 0.609 5.608 3134 Z= 0.321 Chirality : 0.044 0.157 364 Planarity : 0.005 0.053 389 Dihedral : 4.480 16.712 319 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.31 % Allowed : 13.88 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: 0.51 (0.51), residues: 292 helix: 1.42 (0.36), residues: 212 sheet: None (None), residues: 0 loop : -2.74 (0.65), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 130 TYR 0.015 0.002 TYR R 66 PHE 0.012 0.002 PHE R 107 TRP 0.005 0.001 TRP R 83 HIS 0.006 0.001 HIS R 302 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 2286) covalent geometry : angle 0.60671 ( 3132) SS BOND : bond 0.00051 ( 1) SS BOND : angle 2.36110 ( 2) hydrogen bonds : bond 0.04612 ( 169) hydrogen bonds : angle 4.59778 ( 498) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.086 Fit side-chains REVERT: R 102 TYR cc_start: 0.7921 (m-80) cc_final: 0.7323 (m-80) REVERT: R 169 PHE cc_start: 0.6261 (OUTLIER) cc_final: 0.5885 (m-10) REVERT: R 244 LEU cc_start: 0.7668 (tp) cc_final: 0.7395 (tp) outliers start: 9 outliers final: 5 residues processed: 46 average time/residue: 0.0696 time to fit residues: 3.7748 Evaluate side-chains 47 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain R residue 295 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 16 optimal weight: 0.0970 chunk 11 optimal weight: 0.4980 chunk 18 optimal weight: 0.2980 chunk 4 optimal weight: 0.0870 chunk 23 optimal weight: 0.2980 chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 0.0970 chunk 6 optimal weight: 0.5980 chunk 21 optimal weight: 0.0770 chunk 1 optimal weight: 0.0980 chunk 12 optimal weight: 0.2980 overall best weight: 0.0912 ------------------------------------------------------------------------------- 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 = 0.3858 r_free = 0.3858 target = 0.146608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.133722 restraints weight = 3037.430| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 1.33 r_work: 0.3615 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2287 Z= 0.122 Angle : 0.544 5.647 3134 Z= 0.288 Chirality : 0.040 0.114 364 Planarity : 0.005 0.051 389 Dihedral : 4.096 15.007 319 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.35 % Allowed : 16.27 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: 1.03 (0.51), residues: 292 helix: 1.80 (0.37), residues: 212 sheet: None (None), residues: 0 loop : -2.54 (0.65), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 130 TYR 0.014 0.001 TYR R 66 PHE 0.012 0.001 PHE R 107 TRP 0.008 0.001 TRP R 194 HIS 0.003 0.001 HIS R 269 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 2286) covalent geometry : angle 0.54352 ( 3132) SS BOND : bond 0.00113 ( 1) SS BOND : angle 1.20752 ( 2) hydrogen bonds : bond 0.03629 ( 169) hydrogen bonds : angle 4.36811 ( 498) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.078 Fit side-chains REVERT: R 102 TYR cc_start: 0.7820 (m-80) cc_final: 0.7206 (m-80) REVERT: R 116 TYR cc_start: 0.8173 (t80) cc_final: 0.7714 (t80) REVERT: R 121 HIS cc_start: 0.7637 (m170) cc_final: 0.7360 (m-70) REVERT: R 169 PHE cc_start: 0.6108 (OUTLIER) cc_final: 0.5718 (m-10) REVERT: R 244 LEU cc_start: 0.7596 (tp) cc_final: 0.7361 (mt) outliers start: 7 outliers final: 3 residues processed: 45 average time/residue: 0.0602 time to fit residues: 3.2127 Evaluate side-chains 45 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 MET Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 228 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 4 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 0.0980 chunk 10 optimal weight: 0.3980 chunk 2 optimal weight: 0.0770 chunk 3 optimal weight: 0.2980 chunk 8 optimal weight: 0.6980 chunk 14 optimal weight: 0.4980 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 0.0970 overall best weight: 0.1936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.145363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.132642 restraints weight = 2947.231| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.30 r_work: 0.3602 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2287 Z= 0.141 Angle : 0.556 5.691 3134 Z= 0.293 Chirality : 0.040 0.119 364 Planarity : 0.005 0.050 389 Dihedral : 4.118 15.298 319 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.31 % Allowed : 15.79 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: 1.19 (0.51), residues: 292 helix: 1.92 (0.36), residues: 211 sheet: None (None), residues: 0 loop : -2.44 (0.66), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 130 TYR 0.013 0.002 TYR R 66 PHE 0.013 0.002 PHE R 237 TRP 0.009 0.001 TRP R 83 HIS 0.006 0.001 HIS R 79 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 2286) covalent geometry : angle 0.55486 ( 3132) SS BOND : bond 0.00038 ( 1) SS BOND : angle 1.23034 ( 2) hydrogen bonds : bond 0.03996 ( 169) hydrogen bonds : angle 4.33538 ( 498) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.083 Fit side-chains REVERT: R 102 TYR cc_start: 0.7853 (m-80) cc_final: 0.7241 (m-80) REVERT: R 121 HIS cc_start: 0.7657 (m170) cc_final: 0.7387 (m-70) REVERT: R 169 PHE cc_start: 0.6104 (OUTLIER) cc_final: 0.5704 (m-10) REVERT: R 272 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7746 (mp) outliers start: 9 outliers final: 4 residues processed: 46 average time/residue: 0.0689 time to fit residues: 3.7023 Evaluate side-chains 46 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 MET Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 280 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 21 optimal weight: 0.0870 chunk 13 optimal weight: 0.0870 chunk 10 optimal weight: 0.0980 chunk 22 optimal weight: 0.2980 chunk 9 optimal weight: 0.0770 chunk 20 optimal weight: 0.0070 chunk 18 optimal weight: 0.0980 chunk 17 optimal weight: 0.1980 chunk 24 optimal weight: 0.0570 chunk 3 optimal weight: 0.0980 chunk 28 optimal weight: 0.0370 overall best weight: 0.0530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 58 ASN R 149 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.149880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.137216 restraints weight = 3016.614| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.33 r_work: 0.3664 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3555 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2287 Z= 0.112 Angle : 0.529 5.656 3134 Z= 0.278 Chirality : 0.039 0.112 364 Planarity : 0.005 0.049 389 Dihedral : 3.889 14.272 319 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.39 % Allowed : 20.10 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: 1.51 (0.51), residues: 292 helix: 2.15 (0.36), residues: 212 sheet: None (None), residues: 0 loop : -2.32 (0.65), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 130 TYR 0.013 0.001 TYR R 66 PHE 0.012 0.001 PHE R 107 TRP 0.009 0.001 TRP R 194 HIS 0.004 0.001 HIS R 269 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 2286) covalent geometry : angle 0.52852 ( 3132) SS BOND : bond 0.00116 ( 1) SS BOND : angle 0.72691 ( 2) hydrogen bonds : bond 0.03272 ( 169) hydrogen bonds : angle 4.18481 ( 498) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.087 Fit side-chains REVERT: R 27 VAL cc_start: 0.6604 (t) cc_final: 0.6125 (t) REVERT: R 102 TYR cc_start: 0.7718 (m-80) cc_final: 0.7155 (m-80) REVERT: R 116 TYR cc_start: 0.8013 (t80) cc_final: 0.7598 (t80) REVERT: R 169 PHE cc_start: 0.5951 (OUTLIER) cc_final: 0.5582 (m-10) REVERT: R 272 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7719 (mp) outliers start: 5 outliers final: 3 residues processed: 36 average time/residue: 0.0570 time to fit residues: 2.5219 Evaluate side-chains 36 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 MET Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain R residue 272 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 20 optimal weight: 0.0270 chunk 5 optimal weight: 0.1980 chunk 18 optimal weight: 0.5980 chunk 7 optimal weight: 0.0870 chunk 25 optimal weight: 0.5980 chunk 13 optimal weight: 0.0970 chunk 22 optimal weight: 0.3980 chunk 4 optimal weight: 0.2980 chunk 27 optimal weight: 0.0030 chunk 15 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 overall best weight: 0.0824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.149472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.136946 restraints weight = 3037.386| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 1.34 r_work: 0.3658 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2287 Z= 0.114 Angle : 0.522 5.718 3134 Z= 0.276 Chirality : 0.039 0.114 364 Planarity : 0.005 0.049 389 Dihedral : 3.831 14.302 319 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.87 % Allowed : 20.10 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: 1.65 (0.51), residues: 292 helix: 2.23 (0.36), residues: 212 sheet: None (None), residues: 0 loop : -2.24 (0.65), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 130 TYR 0.011 0.001 TYR R 66 PHE 0.011 0.001 PHE R 107 TRP 0.010 0.001 TRP R 83 HIS 0.005 0.001 HIS R 79 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 2286) covalent geometry : angle 0.52196 ( 3132) SS BOND : bond 0.00067 ( 1) SS BOND : angle 0.80522 ( 2) hydrogen bonds : bond 0.03368 ( 169) hydrogen bonds : angle 4.08894 ( 498) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.054 Fit side-chains REVERT: R 27 VAL cc_start: 0.6545 (t) cc_final: 0.6069 (t) REVERT: R 102 TYR cc_start: 0.7777 (m-80) cc_final: 0.7190 (m-80) REVERT: R 116 TYR cc_start: 0.8205 (t80) cc_final: 0.7699 (t80) REVERT: R 121 HIS cc_start: 0.7702 (m90) cc_final: 0.7463 (m-70) REVERT: R 169 PHE cc_start: 0.5974 (OUTLIER) cc_final: 0.5570 (m-10) REVERT: R 181 MET cc_start: 0.7959 (tpt) cc_final: 0.7749 (tpp) REVERT: R 272 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7724 (mp) outliers start: 6 outliers final: 3 residues processed: 35 average time/residue: 0.0542 time to fit residues: 2.3144 Evaluate side-chains 35 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 MET Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain R residue 272 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 21 optimal weight: 0.1980 chunk 11 optimal weight: 0.0060 chunk 0 optimal weight: 1.9990 chunk 20 optimal weight: 0.0070 chunk 12 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 overall best weight: 0.2814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.144845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.132256 restraints weight = 3024.818| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 1.32 r_work: 0.3598 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2287 Z= 0.167 Angle : 0.567 5.846 3134 Z= 0.303 Chirality : 0.041 0.119 364 Planarity : 0.005 0.050 389 Dihedral : 4.023 15.066 319 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.87 % Allowed : 20.10 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: 1.48 (0.50), residues: 292 helix: 2.08 (0.35), residues: 211 sheet: None (None), residues: 0 loop : -2.14 (0.68), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 130 TYR 0.012 0.002 TYR R 66 PHE 0.011 0.002 PHE R 97 TRP 0.011 0.001 TRP R 83 HIS 0.005 0.001 HIS R 302 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 2286) covalent geometry : angle 0.56661 ( 3132) SS BOND : bond 0.00103 ( 1) SS BOND : angle 1.11217 ( 2) hydrogen bonds : bond 0.04274 ( 169) hydrogen bonds : angle 4.32947 ( 498) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.062 Fit side-chains REVERT: R 102 TYR cc_start: 0.7876 (m-80) cc_final: 0.7282 (m-80) REVERT: R 169 PHE cc_start: 0.6054 (OUTLIER) cc_final: 0.5693 (m-10) REVERT: R 187 PHE cc_start: 0.7810 (m-80) cc_final: 0.7288 (m-80) REVERT: R 272 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7782 (mp) outliers start: 6 outliers final: 3 residues processed: 47 average time/residue: 0.0506 time to fit residues: 2.9165 Evaluate side-chains 50 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 MET Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain R residue 272 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 8 optimal weight: 0.7980 chunk 13 optimal weight: 0.1980 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 28 optimal weight: 0.2980 chunk 17 optimal weight: 0.0770 chunk 6 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 0.4980 chunk 19 optimal weight: 0.3980 overall best weight: 0.2738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS R 269 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.145577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.131624 restraints weight = 2951.115| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 1.36 r_work: 0.3603 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2287 Z= 0.168 Angle : 0.578 5.811 3134 Z= 0.308 Chirality : 0.042 0.117 364 Planarity : 0.005 0.049 389 Dihedral : 4.124 15.993 319 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.39 % Allowed : 20.57 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: 1.45 (0.50), residues: 292 helix: 2.06 (0.35), residues: 211 sheet: None (None), residues: 0 loop : -2.16 (0.69), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 130 TYR 0.013 0.002 TYR R 66 PHE 0.010 0.001 PHE R 107 TRP 0.014 0.001 TRP R 83 HIS 0.005 0.001 HIS R 79 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 2286) covalent geometry : angle 0.57456 ( 3132) SS BOND : bond 0.00012 ( 1) SS BOND : angle 2.61092 ( 2) hydrogen bonds : bond 0.04340 ( 169) hydrogen bonds : angle 4.36341 ( 498) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.059 Fit side-chains REVERT: R 102 TYR cc_start: 0.7870 (m-80) cc_final: 0.7288 (m-80) REVERT: R 169 PHE cc_start: 0.6106 (OUTLIER) cc_final: 0.5734 (m-10) REVERT: R 272 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7750 (mp) outliers start: 5 outliers final: 3 residues processed: 43 average time/residue: 0.0520 time to fit residues: 2.6781 Evaluate side-chains 43 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 MET Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain R residue 272 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 3 optimal weight: 0.0980 chunk 22 optimal weight: 0.4980 chunk 23 optimal weight: 0.0770 chunk 26 optimal weight: 0.2980 chunk 18 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 10 optimal weight: 0.0980 chunk 15 optimal weight: 0.2980 chunk 4 optimal weight: 0.2980 chunk 28 optimal weight: 0.7980 overall best weight: 0.1738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.145836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.133225 restraints weight = 2998.447| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 1.33 r_work: 0.3614 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2287 Z= 0.140 Angle : 0.572 5.727 3134 Z= 0.298 Chirality : 0.040 0.115 364 Planarity : 0.005 0.049 389 Dihedral : 4.077 15.804 319 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.35 % Allowed : 20.57 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: 1.44 (0.50), residues: 292 helix: 2.05 (0.35), residues: 213 sheet: None (None), residues: 0 loop : -2.27 (0.69), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 130 TYR 0.013 0.002 TYR R 66 PHE 0.011 0.001 PHE R 107 TRP 0.012 0.001 TRP R 83 HIS 0.006 0.001 HIS R 79 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 2286) covalent geometry : angle 0.57000 ( 3132) SS BOND : bond 0.00094 ( 1) SS BOND : angle 2.01725 ( 2) hydrogen bonds : bond 0.03957 ( 169) hydrogen bonds : angle 4.28646 ( 498) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 978.55 seconds wall clock time: 17 minutes 20.36 seconds (1040.36 seconds total)