Starting phenix.real_space_refine on Fri May 9 12:45:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jgc_36230/05_2025/8jgc_36230.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jgc_36230/05_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_36230/05_2025/8jgc_36230.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jgc_36230/05_2025/8jgc_36230.map" model { file = "/net/cci-nas-00/data/ceres_data/8jgc_36230/05_2025/8jgc_36230.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jgc_36230/05_2025/8jgc_36230.cif" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 3.69, per 1000 atoms: 2.43 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: 0.38 Conformation dependent library (CDL) restraints added in 212.3 milliseconds 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: 0.16 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: 0.33 Time building geometry restraints manager: 0.45 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: 6.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.540 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.580 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.035 0.009 TRP A 167 HIS 0.004 0.001 HIS A 10 PHE 0.016 0.003 PHE A 86 TYR 0.006 0.003 TYR A 107 ARG 0.001 0.000 ARG A 201 Details of bonding type rmsd hydrogen bonds : bond 0.13558 ( 61) hydrogen bonds : angle 6.96054 ( 183) SS BOND : bond 0.00476 ( 1) SS BOND : angle 0.82821 ( 2) covalent geometry : bond 0.00796 ( 1545) covalent geometry : angle 1.04544 ( 2084) *********************** 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 : 0.184 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: 0.1156 time to fit residues: 3.8562 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 : 0.179 ------------------------------------------------------------------------------- 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 16 optimal weight: 0.2980 chunk 15 optimal weight: 0.9980 chunk 8 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 19 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 = 34)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.104174 restraints weight = 1877.928| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.27 r_work: 0.3289 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (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 TRP 0.004 0.001 TRP A 167 HIS 0.003 0.001 HIS A 10 PHE 0.017 0.002 PHE A 196 TYR 0.002 0.001 TYR A 107 ARG 0.001 0.000 ARG A 201 Details of bonding type rmsd hydrogen bonds : bond 0.03432 ( 61) hydrogen bonds : angle 4.82343 ( 183) SS BOND : bond 0.00200 ( 1) SS BOND : angle 1.20184 ( 2) covalent geometry : bond 0.00241 ( 1545) covalent geometry : angle 0.53349 ( 2084) *********************** 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 : 0.178 Fit side-chains REVERT: A 17 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.7139 (mtm-85) REVERT: A 112 MET cc_start: 0.4760 (ttt) cc_final: 0.4302 (ttp) REVERT: A 144 MET cc_start: 0.7972 (ttp) cc_final: 0.7538 (ttm) REVERT: A 191 GLU cc_start: 0.8424 (tm-30) cc_final: 0.8120 (tm-30) outliers start: 6 outliers final: 3 residues processed: 33 average time/residue: 0.1221 time to fit residues: 4.7266 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 : 0.173 ------------------------------------------------------------------------------- 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 4 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 = 0.126125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.107512 restraints weight = 1883.154| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.27 r_work: 0.3241 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 1546 Z= 0.152 Angle : 0.579 4.059 2086 Z= 0.304 Chirality : 0.051 0.146 244 Planarity : 0.006 0.038 263 Dihedral : 7.514 50.905 212 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.40 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.60), residues: 200 helix: -0.54 (0.52), residues: 91 sheet: 0.05 (1.25), residues: 23 loop : -2.21 (0.70), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 167 HIS 0.003 0.001 HIS A 10 PHE 0.010 0.002 PHE A 86 TYR 0.005 0.002 TYR A 107 ARG 0.002 0.001 ARG A 77 Details of bonding type rmsd hydrogen bonds : bond 0.03504 ( 61) hydrogen bonds : angle 4.63990 ( 183) SS BOND : bond 0.00505 ( 1) SS BOND : angle 0.83658 ( 2) covalent geometry : bond 0.00376 ( 1545) covalent geometry : angle 0.57841 ( 2084) *********************** 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 : 0.185 Fit side-chains REVERT: A 112 MET cc_start: 0.4923 (ttt) cc_final: 0.4499 (ttp) REVERT: A 144 MET cc_start: 0.8043 (ttp) cc_final: 0.7597 (ttm) REVERT: A 191 GLU cc_start: 0.8340 (tm-30) cc_final: 0.8039 (tm-30) outliers start: 4 outliers final: 3 residues processed: 25 average time/residue: 0.1472 time to fit residues: 4.2817 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 : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 17 ARG 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 19 optimal weight: 2.9990 chunk 14 optimal weight: 0.0770 chunk 16 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 = 0.3684 r_free = 0.3684 target = 0.124925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.106928 restraints weight = 1917.151| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.97 r_work: 0.3361 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2074 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= 0.090 Angle : 0.468 3.272 2086 Z= 0.246 Chirality : 0.046 0.133 244 Planarity : 0.005 0.035 263 Dihedral : 5.838 42.289 210 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.81 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.62), residues: 200 helix: -0.22 (0.52), residues: 93 sheet: 0.96 (1.30), residues: 22 loop : -1.67 (0.73), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 167 HIS 0.003 0.001 HIS A 10 PHE 0.011 0.001 PHE A 196 TYR 0.003 0.001 TYR A 107 ARG 0.001 0.000 ARG A 17 Details of bonding type rmsd hydrogen bonds : bond 0.02692 ( 61) hydrogen bonds : angle 4.22592 ( 183) SS BOND : bond 0.00402 ( 1) SS BOND : angle 0.72911 ( 2) covalent geometry : bond 0.00207 ( 1545) covalent geometry : angle 0.46808 ( 2084) *********************** 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 29 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.191 Fit side-chains REVERT: A 17 ARG cc_start: 0.7285 (tpp-160) cc_final: 0.6714 (mtm-85) REVERT: A 92 LEU cc_start: 0.8392 (mt) cc_final: 0.8168 (mm) REVERT: A 112 MET cc_start: 0.4967 (ttt) cc_final: 0.4552 (ttp) REVERT: A 144 MET cc_start: 0.7743 (ttp) cc_final: 0.7403 (ttm) REVERT: A 191 GLU cc_start: 0.8336 (tm-30) cc_final: 0.8065 (tm-30) outliers start: 3 outliers final: 3 residues processed: 29 average time/residue: 0.1622 time to fit residues: 5.3669 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 : 0.157 ------------------------------------------------------------------------------- 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 13 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.3584 r_free = 0.3584 target = 0.120192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.100462 restraints weight = 1936.365| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.39 r_work: 0.3233 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 1546 Z= 0.156 Angle : 0.551 3.782 2086 Z= 0.287 Chirality : 0.050 0.143 244 Planarity : 0.005 0.040 263 Dihedral : 4.551 21.887 206 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.60), residues: 200 helix: -0.24 (0.52), residues: 93 sheet: 0.69 (1.28), residues: 22 loop : -1.70 (0.70), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 167 HIS 0.003 0.001 HIS A 10 PHE 0.010 0.002 PHE A 86 TYR 0.005 0.002 TYR A 107 ARG 0.002 0.001 ARG A 17 Details of bonding type rmsd hydrogen bonds : bond 0.03393 ( 61) hydrogen bonds : angle 4.45545 ( 183) SS BOND : bond 0.00401 ( 1) SS BOND : angle 0.56525 ( 2) covalent geometry : bond 0.00392 ( 1545) covalent geometry : angle 0.55065 ( 2084) *********************** 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 22 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.178 Fit side-chains REVERT: A 112 MET cc_start: 0.4845 (ttt) cc_final: 0.4399 (ttp) REVERT: A 144 MET cc_start: 0.7882 (ttp) cc_final: 0.7496 (ttm) REVERT: A 191 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7759 (tm-30) outliers start: 2 outliers final: 2 residues processed: 22 average time/residue: 0.1613 time to fit residues: 4.1293 Evaluate side-chains 21 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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 1 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 17 optimal weight: 0.0970 chunk 9 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 overall best weight: 1.1380 ------------------------------------------------------------------------------- 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 = 0.3615 r_free = 0.3615 target = 0.122477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.102674 restraints weight = 1949.556| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.39 r_work: 0.3269 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1546 Z= 0.104 Angle : 0.478 3.433 2086 Z= 0.250 Chirality : 0.047 0.132 244 Planarity : 0.005 0.037 263 Dihedral : 3.982 13.719 205 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.48 % Allowed : 15.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.61), residues: 200 helix: 0.05 (0.52), residues: 93 sheet: 0.97 (1.31), residues: 22 loop : -1.36 (0.72), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 167 HIS 0.003 0.001 HIS A 10 PHE 0.008 0.001 PHE A 57 TYR 0.003 0.001 TYR A 107 ARG 0.001 0.000 ARG A 77 Details of bonding type rmsd hydrogen bonds : bond 0.02846 ( 61) hydrogen bonds : angle 4.27673 ( 183) SS BOND : bond 0.00071 ( 1) SS BOND : angle 0.59022 ( 2) covalent geometry : bond 0.00254 ( 1545) covalent geometry : angle 0.47792 ( 2084) *********************** 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 25 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.179 Fit side-chains REVERT: A 92 LEU cc_start: 0.8424 (mt) cc_final: 0.8113 (mm) REVERT: A 112 MET cc_start: 0.4683 (ttt) cc_final: 0.4246 (ttp) REVERT: A 144 MET cc_start: 0.7776 (ttp) cc_final: 0.7455 (ttm) REVERT: A 191 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7774 (tm-30) outliers start: 4 outliers final: 3 residues processed: 25 average time/residue: 0.1537 time to fit residues: 4.4530 Evaluate side-chains 22 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.160 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 11 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 8 optimal weight: 0.7980 chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.120547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.101803 restraints weight = 2042.357| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.07 r_work: 0.3257 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1546 Z= 0.107 Angle : 0.492 3.531 2086 Z= 0.258 Chirality : 0.047 0.131 244 Planarity : 0.005 0.036 263 Dihedral : 3.937 13.644 205 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.62), residues: 200 helix: 0.18 (0.52), residues: 93 sheet: 1.00 (1.32), residues: 22 loop : -1.26 (0.73), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 167 HIS 0.002 0.001 HIS A 10 PHE 0.008 0.001 PHE A 57 TYR 0.003 0.001 TYR A 107 ARG 0.002 0.001 ARG A 17 Details of bonding type rmsd hydrogen bonds : bond 0.02802 ( 61) hydrogen bonds : angle 4.24528 ( 183) SS BOND : bond 0.00108 ( 1) SS BOND : angle 0.52364 ( 2) covalent geometry : bond 0.00262 ( 1545) covalent geometry : angle 0.49158 ( 2084) *********************** 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 25 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.138 Fit side-chains REVERT: A 92 LEU cc_start: 0.8373 (mt) cc_final: 0.8116 (mm) REVERT: A 112 MET cc_start: 0.4950 (ttt) cc_final: 0.4508 (ttp) REVERT: A 144 MET cc_start: 0.7777 (ttp) cc_final: 0.7423 (ttm) REVERT: A 191 GLU cc_start: 0.8368 (tm-30) cc_final: 0.8108 (tm-30) outliers start: 3 outliers final: 3 residues processed: 25 average time/residue: 0.0870 time to fit residues: 2.6626 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 : 0.136 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 8 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 12 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.3591 r_free = 0.3591 target = 0.118633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.100619 restraints weight = 1991.727| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.01 r_work: 0.3250 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2437 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= 0.121 Angle : 0.500 4.430 2086 Z= 0.261 Chirality : 0.048 0.134 244 Planarity : 0.005 0.036 263 Dihedral : 4.014 14.754 205 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.86 % Allowed : 16.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.61), residues: 200 helix: 0.16 (0.52), residues: 93 sheet: 0.88 (1.31), residues: 22 loop : -1.33 (0.71), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 167 HIS 0.003 0.001 HIS A 10 PHE 0.008 0.001 PHE A 57 TYR 0.004 0.001 TYR A 107 ARG 0.002 0.001 ARG A 17 Details of bonding type rmsd hydrogen bonds : bond 0.02965 ( 61) hydrogen bonds : angle 4.35840 ( 183) SS BOND : bond 0.00259 ( 1) SS BOND : angle 0.50646 ( 2) covalent geometry : bond 0.00298 ( 1545) covalent geometry : angle 0.50022 ( 2084) *********************** 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 24 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.168 Fit side-chains REVERT: A 92 LEU cc_start: 0.8350 (mt) cc_final: 0.8118 (mm) REVERT: A 112 MET cc_start: 0.5002 (ttt) cc_final: 0.4559 (ttp) REVERT: A 144 MET cc_start: 0.7861 (ttp) cc_final: 0.7500 (ttm) REVERT: A 191 GLU cc_start: 0.8356 (tm-30) cc_final: 0.8073 (tm-30) outliers start: 3 outliers final: 3 residues processed: 24 average time/residue: 0.1051 time to fit residues: 3.1018 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 : 0.166 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 14 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 16 optimal weight: 0.1980 chunk 6 optimal weight: 0.7980 chunk 4 optimal weight: 0.0970 chunk 7 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.121302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.102700 restraints weight = 2031.697| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.10 r_work: 0.3275 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2625 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= 0.096 Angle : 0.479 6.055 2086 Z= 0.250 Chirality : 0.046 0.127 244 Planarity : 0.005 0.034 263 Dihedral : 3.822 12.906 205 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.86 % Allowed : 18.01 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.61), residues: 200 helix: 0.48 (0.52), residues: 94 sheet: 1.12 (1.33), residues: 22 loop : -1.09 (0.72), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 167 HIS 0.002 0.001 HIS A 10 PHE 0.015 0.002 PHE A 99 TYR 0.003 0.001 TYR A 107 ARG 0.005 0.001 ARG A 77 Details of bonding type rmsd hydrogen bonds : bond 0.02692 ( 61) hydrogen bonds : angle 4.19990 ( 183) SS BOND : bond 0.00170 ( 1) SS BOND : angle 0.35234 ( 2) covalent geometry : bond 0.00231 ( 1545) covalent geometry : angle 0.47895 ( 2084) *********************** 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 25 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.165 Fit side-chains REVERT: A 92 LEU cc_start: 0.8346 (mt) cc_final: 0.8094 (mm) REVERT: A 112 MET cc_start: 0.4962 (ttt) cc_final: 0.4531 (ttp) REVERT: A 144 MET cc_start: 0.7726 (ttp) cc_final: 0.7434 (ttm) REVERT: A 191 GLU cc_start: 0.8341 (tm-30) cc_final: 0.8051 (tm-30) outliers start: 3 outliers final: 3 residues processed: 25 average time/residue: 0.1093 time to fit residues: 3.3227 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 : 0.175 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 7 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 12 optimal weight: 0.3980 chunk 1 optimal weight: 0.0040 chunk 2 optimal weight: 5.9990 overall best weight: 1.2194 ------------------------------------------------------------------------------- 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 = 0.3608 r_free = 0.3608 target = 0.120125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.101633 restraints weight = 2047.849| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.10 r_work: 0.3259 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1546 Z= 0.111 Angle : 0.508 5.983 2086 Z= 0.260 Chirality : 0.047 0.129 244 Planarity : 0.005 0.034 263 Dihedral : 3.907 13.577 205 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.86 % Allowed : 18.63 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.62), residues: 200 helix: 0.54 (0.52), residues: 94 sheet: 0.95 (1.30), residues: 22 loop : -1.09 (0.73), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 167 HIS 0.003 0.001 HIS A 10 PHE 0.009 0.002 PHE A 196 TYR 0.003 0.001 TYR A 107 ARG 0.006 0.001 ARG A 77 Details of bonding type rmsd hydrogen bonds : bond 0.02894 ( 61) hydrogen bonds : angle 4.26602 ( 183) SS BOND : bond 0.00134 ( 1) SS BOND : angle 0.32765 ( 2) covalent geometry : bond 0.00272 ( 1545) covalent geometry : angle 0.50837 ( 2084) ********************** 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 : 0.158 Fit side-chains REVERT: A 92 LEU cc_start: 0.8358 (mt) cc_final: 0.8107 (mm) REVERT: A 112 MET cc_start: 0.4951 (ttt) cc_final: 0.4524 (ttp) REVERT: A 144 MET cc_start: 0.7787 (ttp) cc_final: 0.7488 (ttm) REVERT: A 191 GLU cc_start: 0.8359 (tm-30) cc_final: 0.8063 (tm-30) outliers start: 3 outliers final: 3 residues processed: 24 average time/residue: 0.1021 time to fit residues: 2.9968 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 : 0.174 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 7 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.116589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.098019 restraints weight = 2146.875| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.15 r_work: 0.3200 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 1546 Z= 0.180 Angle : 0.587 6.028 2086 Z= 0.305 Chirality : 0.051 0.139 244 Planarity : 0.005 0.036 263 Dihedral : 4.378 16.726 205 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.86 % Allowed : 17.39 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.60), residues: 200 helix: 0.25 (0.51), residues: 93 sheet: 0.31 (1.29), residues: 23 loop : -1.44 (0.71), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.003 TRP A 167 HIS 0.003 0.001 HIS A 10 PHE 0.012 0.002 PHE A 86 TYR 0.006 0.002 TYR A 107 ARG 0.007 0.002 ARG A 77 Details of bonding type rmsd hydrogen bonds : bond 0.03680 ( 61) hydrogen bonds : angle 4.63895 ( 183) SS BOND : bond 0.00318 ( 1) SS BOND : angle 0.46065 ( 2) covalent geometry : bond 0.00452 ( 1545) covalent geometry : angle 0.58739 ( 2084) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1452.79 seconds wall clock time: 26 minutes 2.19 seconds (1562.19 seconds total)