Starting phenix.real_space_refine on Fri Aug 22 12:37:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jgc_36230/08_2025/8jgc_36230.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jgc_36230/08_2025/8jgc_36230.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jgc_36230/08_2025/8jgc_36230.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jgc_36230/08_2025/8jgc_36230.map" model { file = "/net/cci-nas-00/data/ceres_data/8jgc_36230/08_2025/8jgc_36230.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jgc_36230/08_2025/8jgc_36230.cif" } resolution = 3.44 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= 0.002 sd= 0.028 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 7 5.16 5 C 987 2.51 5 N 249 2.21 5 O 273 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1516 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1516 Classifications: {'peptide': 202} Incomplete info: {'backbone_only': 2} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 191} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 0.48, per 1000 atoms: 0.32 Number of scatterers: 1516 At special positions: 0 Unit cell: (56.43, 51.3, 58.995, 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 7 16.00 O 273 8.00 N 249 7.00 C 987 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 165 " - pdb=" SG CYS A 203 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.07 Conformation dependent library (CDL) restraints added in 38.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 362 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 2 sheets defined 45.5% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 22 through 35 Processing helix chain 'A' and resid 47 through 62 removed outlier: 5.273A pdb=" N PHE A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LEU A 58 " --> pdb=" O GLU A 54 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET A 61 " --> pdb=" O PHE A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 82 Processing helix chain 'A' and resid 93 through 104 Processing helix chain 'A' and resid 113 through 122 Processing helix chain 'A' and resid 185 through 203 removed outlier: 3.892A pdb=" N GLU A 191 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LYS A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A 196 " --> pdb=" O LYS A 192 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU A 198 " --> pdb=" O LYS A 194 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 16 removed outlier: 3.687A pdb=" N THR A 42 " --> pdb=" O LEU A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 88 61 hydrogen bonds defined for protein. 183 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: 0.15 Time building geometry restraints manager: 0.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 291 1.33 - 1.45: 328 1.45 - 1.57: 914 1.57 - 1.70: 0 1.70 - 1.82: 12 Bond restraints: 1545 Sorted by residual: bond pdb=" C VAL A 182 " pdb=" O VAL A 182 " ideal model delta sigma weight residual 1.236 1.209 0.027 1.19e-02 7.06e+03 5.33e+00 bond pdb=" C LEU A 128 " pdb=" O LEU A 128 " ideal model delta sigma weight residual 1.234 1.202 0.032 1.51e-02 4.39e+03 4.56e+00 bond pdb=" CA VAL A 15 " pdb=" C VAL A 15 " ideal model delta sigma weight residual 1.523 1.497 0.026 1.27e-02 6.20e+03 4.10e+00 bond pdb=" CA LEU A 16 " pdb=" C LEU A 16 " ideal model delta sigma weight residual 1.524 1.500 0.024 1.23e-02 6.61e+03 3.83e+00 bond pdb=" CA ILE A 127 " pdb=" CB ILE A 127 " ideal model delta sigma weight residual 1.537 1.513 0.024 1.26e-02 6.30e+03 3.61e+00 ... (remaining 1540 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 1962 2.12 - 4.24: 107 4.24 - 6.36: 12 6.36 - 8.48: 2 8.48 - 10.60: 1 Bond angle restraints: 2084 Sorted by residual: angle pdb=" N VAL A 182 " pdb=" CA VAL A 182 " pdb=" C VAL A 182 " ideal model delta sigma weight residual 109.34 119.94 -10.60 2.08e+00 2.31e-01 2.60e+01 angle pdb=" N ALA A 180 " pdb=" CA ALA A 180 " pdb=" C ALA A 180 " ideal model delta sigma weight residual 112.23 106.50 5.73 1.26e+00 6.30e-01 2.07e+01 angle pdb=" N SER A 179 " pdb=" CA SER A 179 " pdb=" C SER A 179 " ideal model delta sigma weight residual 110.80 118.97 -8.17 2.13e+00 2.20e-01 1.47e+01 angle pdb=" N LEU A 128 " pdb=" CA LEU A 128 " pdb=" C LEU A 128 " ideal model delta sigma weight residual 109.65 115.33 -5.68 1.56e+00 4.11e-01 1.33e+01 angle pdb=" N LEU A 16 " pdb=" CA LEU A 16 " pdb=" C LEU A 16 " ideal model delta sigma weight residual 108.73 114.18 -5.45 1.63e+00 3.76e-01 1.12e+01 ... (remaining 2079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.51: 826 15.51 - 31.03: 67 31.03 - 46.54: 24 46.54 - 62.05: 14 62.05 - 77.57: 1 Dihedral angle restraints: 932 sinusoidal: 368 harmonic: 564 Sorted by residual: dihedral pdb=" CB CYS A 165 " pdb=" SG CYS A 165 " pdb=" SG CYS A 203 " pdb=" CB CYS A 203 " ideal model delta sinusoidal sigma weight residual -86.00 -37.13 -48.87 1 1.00e+01 1.00e-02 3.29e+01 dihedral pdb=" CA VAL A 154 " pdb=" C VAL A 154 " pdb=" N PRO A 155 " pdb=" CA PRO A 155 " ideal model delta harmonic sigma weight residual -180.00 -161.75 -18.25 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA MET A 144 " pdb=" C MET A 144 " pdb=" N LYS A 145 " pdb=" CA LYS A 145 " ideal model delta harmonic sigma weight residual 180.00 163.80 16.20 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 168 0.059 - 0.118: 54 0.118 - 0.177: 17 0.177 - 0.236: 3 0.236 - 0.295: 2 Chirality restraints: 244 Sorted by residual: chirality pdb=" CA SER A 179 " pdb=" N SER A 179 " pdb=" C SER A 179 " pdb=" CB SER A 179 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA THR A 126 " pdb=" N THR A 126 " pdb=" C THR A 126 " pdb=" CB THR A 126 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA VAL A 13 " pdb=" N VAL A 13 " pdb=" C VAL A 13 " pdb=" CB VAL A 13 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 241 not shown) Planarity restraints: 263 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 12 " 0.015 2.00e-02 2.50e+03 2.87e-02 8.24e+00 pdb=" C ILE A 12 " -0.050 2.00e-02 2.50e+03 pdb=" O ILE A 12 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL A 13 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 167 " 0.008 2.00e-02 2.50e+03 1.46e-02 5.36e+00 pdb=" CG TRP A 167 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A 167 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP A 167 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 167 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 167 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 167 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 167 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 167 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 167 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 137 " -0.036 5.00e-02 4.00e+02 5.41e-02 4.68e+00 pdb=" N PRO A 138 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 138 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 138 " -0.030 5.00e-02 4.00e+02 ... (remaining 260 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 349 2.78 - 3.31: 1482 3.31 - 3.84: 2330 3.84 - 4.37: 2780 4.37 - 4.90: 4873 Nonbonded interactions: 11814 Sorted by model distance: nonbonded pdb=" N ILE A 65 " pdb=" OE2 GLU A 85 " model vdw 2.251 3.120 nonbonded pdb=" OG SER A 97 " pdb=" NE2 HIS A 125 " model vdw 2.274 3.120 nonbonded pdb=" OD1 ASN A 160 " pdb=" ND2 ASN A 163 " model vdw 2.298 3.120 nonbonded pdb=" CD1 LEU A 16 " pdb=" CG2 VAL A 182 " model vdw 2.306 3.880 nonbonded pdb=" OE2 GLU A 22 " pdb=" CD LYS A 26 " model vdw 2.501 3.440 ... (remaining 11809 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: 7.150 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: 0.020 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 2.670 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:0.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 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 : 0.008 0.051 1546 Z= 0.378 Angle : 1.045 10.602 2086 Z= 0.592 Chirality : 0.068 0.295 244 Planarity : 0.008 0.054 263 Dihedral : 15.174 77.566 567 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 23.58 Ramachandran Plot: Outliers : 1.00 % Allowed : 9.00 % Favored : 90.00 % Rotamer: Outliers : 4.35 % Allowed : 1.86 % Favored : 93.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -3.45 (0.55), residues: 200 helix: -1.91 (0.47), residues: 97 sheet: -1.00 (1.21), residues: 23 loop : -3.06 (0.65), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 201 TYR 0.006 0.003 TYR A 107 PHE 0.016 0.003 PHE A 86 TRP 0.035 0.009 TRP A 167 HIS 0.004 0.001 HIS A 10 Details of bonding type rmsd covalent geometry : bond 0.00796 ( 1545) covalent geometry : angle 1.04544 ( 2084) SS BOND : bond 0.00476 ( 1) SS BOND : angle 0.82821 ( 2) hydrogen bonds : bond 0.13558 ( 61) hydrogen bonds : angle 6.96054 ( 183) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.059 Fit side-chains REVERT: A 49 ASP cc_start: 0.7927 (p0) cc_final: 0.7647 (p0) REVERT: A 112 MET cc_start: 0.4726 (ttt) cc_final: 0.4401 (ttp) REVERT: A 191 GLU cc_start: 0.7528 (tm-30) cc_final: 0.7305 (tm-30) outliers start: 7 outliers final: 5 residues processed: 28 average time/residue: 0.0337 time to fit residues: 1.1412 Evaluate side-chains 27 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 179 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3624 r_free = 0.3624 target = 0.123062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.104137 restraints weight = 1888.182| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.28 r_work: 0.3287 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 1546 Z= 0.106 Angle : 0.535 3.708 2086 Z= 0.282 Chirality : 0.048 0.141 244 Planarity : 0.006 0.039 263 Dihedral : 8.193 57.522 215 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.73 % Allowed : 6.83 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.80 (0.60), residues: 200 helix: -0.74 (0.51), residues: 91 sheet: -0.33 (1.12), residues: 27 loop : -1.94 (0.74), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 201 TYR 0.002 0.001 TYR A 107 PHE 0.017 0.002 PHE A 196 TRP 0.004 0.001 TRP A 167 HIS 0.003 0.001 HIS A 10 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 1545) covalent geometry : angle 0.53349 ( 2084) SS BOND : bond 0.00200 ( 1) SS BOND : angle 1.20184 ( 2) hydrogen bonds : bond 0.03432 ( 61) hydrogen bonds : angle 4.82343 ( 183) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.056 Fit side-chains REVERT: A 17 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.7138 (mtm-85) REVERT: A 112 MET cc_start: 0.4758 (ttt) cc_final: 0.4300 (ttp) REVERT: A 144 MET cc_start: 0.7972 (ttp) cc_final: 0.7538 (ttm) REVERT: A 191 GLU cc_start: 0.8423 (tm-30) cc_final: 0.8119 (tm-30) outliers start: 6 outliers final: 3 residues processed: 33 average time/residue: 0.0695 time to fit residues: 2.6170 Evaluate side-chains 26 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 185 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 16 optimal weight: 0.0000 chunk 17 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 0.3980 chunk 13 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 overall best weight: 1.6790 ------------------------------------------------------------------------------- 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 = 0.3652 r_free = 0.3652 target = 0.126810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.108111 restraints weight = 1880.396| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.24 r_work: 0.3257 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 1546 Z= 0.136 Angle : 0.557 3.819 2086 Z= 0.293 Chirality : 0.050 0.145 244 Planarity : 0.005 0.038 263 Dihedral : 7.408 50.798 212 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.48 % Allowed : 13.04 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.62 (0.61), residues: 200 helix: -0.49 (0.53), residues: 91 sheet: 0.48 (1.27), residues: 22 loop : -2.13 (0.70), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 77 TYR 0.004 0.001 TYR A 107 PHE 0.010 0.002 PHE A 57 TRP 0.006 0.002 TRP A 167 HIS 0.003 0.001 HIS A 10 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 1545) covalent geometry : angle 0.55709 ( 2084) SS BOND : bond 0.00066 ( 1) SS BOND : angle 0.80625 ( 2) hydrogen bonds : bond 0.03330 ( 61) hydrogen bonds : angle 4.57543 ( 183) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.062 Fit side-chains REVERT: A 112 MET cc_start: 0.4918 (ttt) cc_final: 0.4503 (ttp) REVERT: A 144 MET cc_start: 0.8000 (ttp) cc_final: 0.7598 (ttm) REVERT: A 191 GLU cc_start: 0.8349 (tm-30) cc_final: 0.8052 (tm-30) outliers start: 4 outliers final: 2 residues processed: 25 average time/residue: 0.0734 time to fit residues: 2.1208 Evaluate side-chains 23 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 185 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 3 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3627 r_free = 0.3627 target = 0.122988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.103419 restraints weight = 1921.502| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.32 r_work: 0.3290 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 1546 Z= 0.099 Angle : 0.483 3.386 2086 Z= 0.253 Chirality : 0.047 0.135 244 Planarity : 0.005 0.035 263 Dihedral : 4.461 25.678 206 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.86 % Allowed : 14.29 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.23 (0.61), residues: 200 helix: -0.29 (0.52), residues: 93 sheet: 0.81 (1.29), residues: 22 loop : -1.82 (0.73), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 201 TYR 0.003 0.001 TYR A 107 PHE 0.009 0.001 PHE A 196 TRP 0.004 0.001 TRP A 167 HIS 0.003 0.001 HIS A 10 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 1545) covalent geometry : angle 0.48296 ( 2084) SS BOND : bond 0.00214 ( 1) SS BOND : angle 0.66626 ( 2) hydrogen bonds : bond 0.02819 ( 61) hydrogen bonds : angle 4.30203 ( 183) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.064 Fit side-chains REVERT: A 92 LEU cc_start: 0.8380 (mt) cc_final: 0.8152 (mm) REVERT: A 112 MET cc_start: 0.4863 (ttt) cc_final: 0.4441 (ttp) REVERT: A 144 MET cc_start: 0.7671 (ttp) cc_final: 0.7323 (ttm) REVERT: A 191 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7758 (tm-30) outliers start: 3 outliers final: 3 residues processed: 25 average time/residue: 0.0734 time to fit residues: 2.0918 Evaluate side-chains 21 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 185 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 4 optimal weight: 5.9990 chunk 14 optimal weight: 0.1980 chunk 10 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 15 optimal weight: 0.0980 chunk 3 optimal weight: 5.9990 chunk 17 optimal weight: 0.0970 chunk 18 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.124792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.104917 restraints weight = 1878.161| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.33 r_work: 0.3304 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1546 Z= 0.087 Angle : 0.457 3.522 2086 Z= 0.238 Chirality : 0.046 0.127 244 Planarity : 0.005 0.036 263 Dihedral : 4.072 18.748 206 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.48 % Allowed : 14.29 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.71 (0.62), residues: 200 helix: 0.06 (0.53), residues: 93 sheet: 1.11 (1.31), residues: 22 loop : -1.46 (0.72), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 17 TYR 0.003 0.001 TYR A 107 PHE 0.008 0.001 PHE A 196 TRP 0.003 0.001 TRP A 167 HIS 0.003 0.001 HIS A 10 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 1545) covalent geometry : angle 0.45679 ( 2084) SS BOND : bond 0.00358 ( 1) SS BOND : angle 0.60645 ( 2) hydrogen bonds : bond 0.02585 ( 61) hydrogen bonds : angle 4.13613 ( 183) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.060 Fit side-chains REVERT: A 92 LEU cc_start: 0.8379 (mt) cc_final: 0.8128 (mm) REVERT: A 112 MET cc_start: 0.4801 (ttt) cc_final: 0.4397 (ttp) REVERT: A 144 MET cc_start: 0.7652 (ttp) cc_final: 0.7318 (ttm) REVERT: A 191 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7774 (tm-30) outliers start: 4 outliers final: 2 residues processed: 26 average time/residue: 0.0574 time to fit residues: 1.7488 Evaluate side-chains 20 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 185 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 6 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 17 optimal weight: 0.2980 chunk 12 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 0.0870 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.8560 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.121918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.103705 restraints weight = 1983.645| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.00 r_work: 0.3299 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 1546 Z= 0.097 Angle : 0.470 3.456 2086 Z= 0.245 Chirality : 0.046 0.134 244 Planarity : 0.005 0.037 263 Dihedral : 3.770 12.371 205 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.86 % Allowed : 14.91 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.43 (0.62), residues: 200 helix: 0.25 (0.53), residues: 93 sheet: 1.10 (1.31), residues: 22 loop : -1.23 (0.72), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 17 TYR 0.002 0.001 TYR A 107 PHE 0.008 0.001 PHE A 196 TRP 0.004 0.001 TRP A 167 HIS 0.003 0.001 HIS A 10 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 1545) covalent geometry : angle 0.46983 ( 2084) SS BOND : bond 0.00162 ( 1) SS BOND : angle 0.47936 ( 2) hydrogen bonds : bond 0.02632 ( 61) hydrogen bonds : angle 4.10236 ( 183) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.064 Fit side-chains REVERT: A 112 MET cc_start: 0.5009 (ttt) cc_final: 0.4610 (ttp) REVERT: A 144 MET cc_start: 0.7617 (ttp) cc_final: 0.7330 (ttm) REVERT: A 191 GLU cc_start: 0.8345 (tm-30) cc_final: 0.8075 (tm-30) outliers start: 3 outliers final: 2 residues processed: 23 average time/residue: 0.0497 time to fit residues: 1.3899 Evaluate side-chains 20 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 185 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 4.9990 chunk 10 optimal weight: 0.4980 chunk 17 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 0.0010 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 13 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- 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 = 0.3653 r_free = 0.3653 target = 0.123974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.105566 restraints weight = 1966.391| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.02 r_work: 0.3319 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1546 Z= 0.082 Angle : 0.448 5.031 2086 Z= 0.230 Chirality : 0.045 0.127 244 Planarity : 0.005 0.034 263 Dihedral : 3.612 11.562 205 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.24 % Allowed : 16.15 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.04 (0.63), residues: 200 helix: 0.49 (0.53), residues: 94 sheet: 1.31 (1.33), residues: 22 loop : -0.80 (0.76), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 17 TYR 0.002 0.001 TYR A 107 PHE 0.008 0.001 PHE A 196 TRP 0.002 0.001 TRP A 167 HIS 0.002 0.001 HIS A 10 Details of bonding type rmsd covalent geometry : bond 0.00188 ( 1545) covalent geometry : angle 0.44766 ( 2084) SS BOND : bond 0.00012 ( 1) SS BOND : angle 0.39869 ( 2) hydrogen bonds : bond 0.02361 ( 61) hydrogen bonds : angle 4.04602 ( 183) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.059 Fit side-chains REVERT: A 92 LEU cc_start: 0.8333 (mt) cc_final: 0.8032 (mm) REVERT: A 112 MET cc_start: 0.4972 (ttt) cc_final: 0.4557 (ttp) REVERT: A 144 MET cc_start: 0.7525 (ttp) cc_final: 0.7230 (ttm) REVERT: A 191 GLU cc_start: 0.8309 (tm-30) cc_final: 0.8022 (tm-30) outliers start: 2 outliers final: 2 residues processed: 24 average time/residue: 0.0516 time to fit residues: 1.4660 Evaluate side-chains 20 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 185 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 1 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 5 optimal weight: 0.0980 chunk 10 optimal weight: 8.9990 chunk 11 optimal weight: 0.0670 overall best weight: 0.7520 ------------------------------------------------------------------------------- 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 = 0.3644 r_free = 0.3644 target = 0.123081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.104914 restraints weight = 1989.056| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.00 r_work: 0.3311 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 1546 Z= 0.092 Angle : 0.469 4.871 2086 Z= 0.240 Chirality : 0.046 0.124 244 Planarity : 0.005 0.034 263 Dihedral : 3.619 11.954 205 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.24 % Allowed : 16.15 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.63), residues: 200 helix: 0.59 (0.53), residues: 94 sheet: 1.34 (1.33), residues: 22 loop : -0.79 (0.76), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 17 TYR 0.003 0.001 TYR A 107 PHE 0.008 0.001 PHE A 196 TRP 0.003 0.001 TRP A 167 HIS 0.003 0.001 HIS A 10 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 1545) covalent geometry : angle 0.46897 ( 2084) SS BOND : bond 0.00196 ( 1) SS BOND : angle 0.37410 ( 2) hydrogen bonds : bond 0.02520 ( 61) hydrogen bonds : angle 4.04411 ( 183) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.061 Fit side-chains REVERT: A 92 LEU cc_start: 0.8311 (mt) cc_final: 0.8022 (mm) REVERT: A 112 MET cc_start: 0.4932 (ttt) cc_final: 0.4521 (ttp) REVERT: A 144 MET cc_start: 0.7589 (ttp) cc_final: 0.7326 (ttm) REVERT: A 191 GLU cc_start: 0.8369 (tm-30) cc_final: 0.8083 (tm-30) outliers start: 2 outliers final: 2 residues processed: 26 average time/residue: 0.0764 time to fit residues: 2.2489 Evaluate side-chains 24 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 185 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 15 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3618 r_free = 0.3618 target = 0.121098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.102779 restraints weight = 2007.019| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.06 r_work: 0.3278 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1546 Z= 0.114 Angle : 0.504 5.951 2086 Z= 0.258 Chirality : 0.047 0.130 244 Planarity : 0.005 0.035 263 Dihedral : 3.797 13.716 205 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.24 % Allowed : 17.39 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.07 (0.62), residues: 200 helix: 0.60 (0.52), residues: 94 sheet: 1.18 (1.33), residues: 22 loop : -0.83 (0.74), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 77 TYR 0.004 0.001 TYR A 107 PHE 0.014 0.002 PHE A 99 TRP 0.005 0.002 TRP A 167 HIS 0.003 0.001 HIS A 10 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 1545) covalent geometry : angle 0.50417 ( 2084) SS BOND : bond 0.00172 ( 1) SS BOND : angle 0.38021 ( 2) hydrogen bonds : bond 0.02898 ( 61) hydrogen bonds : angle 4.20519 ( 183) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.062 Fit side-chains REVERT: A 92 LEU cc_start: 0.8371 (mt) cc_final: 0.8073 (mm) REVERT: A 112 MET cc_start: 0.5009 (ttt) cc_final: 0.4574 (ttp) REVERT: A 144 MET cc_start: 0.7717 (ttp) cc_final: 0.7398 (ttm) REVERT: A 191 GLU cc_start: 0.8360 (tm-30) cc_final: 0.8077 (tm-30) outliers start: 2 outliers final: 2 residues processed: 24 average time/residue: 0.0493 time to fit residues: 1.4191 Evaluate side-chains 22 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 185 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 7 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 11 optimal weight: 0.5980 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 = 0.3575 r_free = 0.3575 target = 0.117645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.099299 restraints weight = 2086.900| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.10 r_work: 0.3223 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 1546 Z= 0.167 Angle : 0.581 5.860 2086 Z= 0.298 Chirality : 0.051 0.139 244 Planarity : 0.005 0.037 263 Dihedral : 4.271 16.093 205 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.86 % Allowed : 16.15 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.40 (0.60), residues: 200 helix: 0.33 (0.51), residues: 93 sheet: 0.86 (1.31), residues: 22 loop : -1.19 (0.71), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 77 TYR 0.007 0.002 TYR A 107 PHE 0.011 0.002 PHE A 86 TRP 0.009 0.003 TRP A 167 HIS 0.003 0.001 HIS A 10 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 1545) covalent geometry : angle 0.58142 ( 2084) SS BOND : bond 0.00300 ( 1) SS BOND : angle 0.50778 ( 2) hydrogen bonds : bond 0.03559 ( 61) hydrogen bonds : angle 4.56416 ( 183) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.050 Fit side-chains REVERT: A 92 LEU cc_start: 0.8408 (mt) cc_final: 0.8131 (mm) REVERT: A 112 MET cc_start: 0.4991 (ttt) cc_final: 0.4602 (ttp) REVERT: A 144 MET cc_start: 0.7973 (ttp) cc_final: 0.7607 (ttm) REVERT: A 191 GLU cc_start: 0.8365 (tm-30) cc_final: 0.8101 (tm-30) outliers start: 3 outliers final: 2 residues processed: 24 average time/residue: 0.0503 time to fit residues: 1.4352 Evaluate side-chains 24 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 185 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3621 r_free = 0.3621 target = 0.121484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.102848 restraints weight = 1970.526| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.06 r_work: 0.3279 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 1546 Z= 0.101 Angle : 0.519 6.449 2086 Z= 0.267 Chirality : 0.047 0.125 244 Planarity : 0.005 0.033 263 Dihedral : 3.913 12.621 205 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.24 % Allowed : 15.53 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.06 (0.62), residues: 200 helix: 0.48 (0.52), residues: 94 sheet: 1.06 (1.32), residues: 22 loop : -0.87 (0.74), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 77 TYR 0.003 0.001 TYR A 107 PHE 0.012 0.002 PHE A 7 TRP 0.004 0.001 TRP A 167 HIS 0.003 0.001 HIS A 10 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 1545) covalent geometry : angle 0.51860 ( 2084) SS BOND : bond 0.00200 ( 1) SS BOND : angle 0.54871 ( 2) hydrogen bonds : bond 0.02893 ( 61) hydrogen bonds : angle 4.26279 ( 183) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 823.76 seconds wall clock time: 15 minutes 14.40 seconds (914.40 seconds total)