Starting phenix.real_space_refine on Wed Mar 5 14:20:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jgc_36230/03_2025/8jgc_36230.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jgc_36230/03_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_36230/03_2025/8jgc_36230.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jgc_36230/03_2025/8jgc_36230.map" model { file = "/net/cci-nas-00/data/ceres_data/8jgc_36230/03_2025/8jgc_36230.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jgc_36230/03_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-5624/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: 4.22, per 1000 atoms: 2.78 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: 0.42 Conformation dependent library (CDL) restraints added in 204.7 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: 0.15 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: 0.42 Time building geometry restraints manager: 0.51 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: 5.410 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.420 Find NCS groups from input model: 0.020 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.860 ------------------------------------------------------------------------------- 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 1545 Z= 0.540 Angle : 1.045 10.602 2084 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 *********************** 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 : 0.183 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: 0.1192 time to fit residues: 3.9721 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 : 0.182 ------------------------------------------------------------------------------- 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: 0.2980 chunk 19 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.123119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.103742 restraints weight = 1892.758| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.35 r_work: 0.3282 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 1545 Z= 0.165 Angle : 0.536 3.704 2084 Z= 0.283 Chirality : 0.048 0.141 244 Planarity : 0.006 0.038 263 Dihedral : 8.291 57.255 215 Min Nonbonded Distance : 2.588 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: -0.75 (0.51), residues: 91 sheet: -0.34 (1.12), residues: 27 loop : -1.92 (0.74), residues: 82 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 0.018 0.001 PHE A 196 TYR 0.002 0.001 TYR A 107 ARG 0.001 0.000 ARG A 201 *********************** 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 : 0.183 Fit side-chains REVERT: A 49 ASP cc_start: 0.8371 (p0) cc_final: 0.8048 (p0) REVERT: A 112 MET cc_start: 0.4761 (ttt) cc_final: 0.4277 (ttp) REVERT: A 144 MET cc_start: 0.7776 (ttp) cc_final: 0.7378 (ttm) REVERT: A 191 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7802 (tm-30) outliers start: 6 outliers final: 3 residues processed: 33 average time/residue: 0.1247 time to fit residues: 4.8234 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 : 0.184 ------------------------------------------------------------------------------- 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 185 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3622 r_free = 0.3622 target = 0.122854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.102989 restraints weight = 1899.706| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.36 r_work: 0.3276 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1545 Z= 0.173 Angle : 0.520 3.460 2084 Z= 0.273 Chirality : 0.049 0.146 244 Planarity : 0.005 0.036 263 Dihedral : 5.766 49.786 208 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.24 % Allowed : 13.66 % Favored : 85.09 % 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: -1.45 (0.61), residues: 200 helix: -0.48 (0.52), residues: 93 sheet: 0.63 (1.27), residues: 22 loop : -1.91 (0.73), 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 0.009 0.001 PHE A 57 TYR 0.003 0.001 TYR A 107 ARG 0.002 0.001 ARG A 17 *********************** 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 24 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.183 Fit side-chains REVERT: A 112 MET cc_start: 0.4882 (ttt) cc_final: 0.4482 (ttp) REVERT: A 144 MET cc_start: 0.7670 (ttp) cc_final: 0.7340 (ttm) REVERT: A 191 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7764 (tm-30) outliers start: 2 outliers final: 2 residues processed: 24 average time/residue: 0.1743 time to fit residues: 4.8059 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 : 0.186 ------------------------------------------------------------------------------- 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 19 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3629 r_free = 0.3629 target = 0.124445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.106136 restraints weight = 1826.566| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.20 r_work: 0.3251 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 1545 Z= 0.264 Angle : 0.562 3.876 2084 Z= 0.294 Chirality : 0.051 0.144 244 Planarity : 0.005 0.037 263 Dihedral : 4.818 26.913 206 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % 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: -1.51 (0.60), residues: 200 helix: -0.35 (0.53), residues: 91 sheet: 0.44 (1.26), residues: 22 loop : -2.08 (0.70), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP A 167 HIS 0.003 0.001 HIS A 10 PHE 0.011 0.002 PHE A 86 TYR 0.005 0.002 TYR A 107 ARG 0.002 0.001 ARG A 17 *********************** 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 26 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.185 Fit side-chains REVERT: A 92 LEU cc_start: 0.8426 (mt) cc_final: 0.8196 (mm) REVERT: A 112 MET cc_start: 0.4919 (ttt) cc_final: 0.4498 (ttp) REVERT: A 144 MET cc_start: 0.8017 (ttp) cc_final: 0.7622 (ttm) REVERT: A 191 GLU cc_start: 0.8324 (tm-30) cc_final: 0.8033 (tm-30) outliers start: 3 outliers final: 3 residues processed: 26 average time/residue: 0.1515 time to fit residues: 4.5616 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 : 0.183 ------------------------------------------------------------------------------- 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: 0.8980 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 5 optimal weight: 0.0470 chunk 15 optimal weight: 0.7980 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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 = 0.3634 r_free = 0.3634 target = 0.123871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.104104 restraints weight = 1859.844| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.32 r_work: 0.3295 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 1545 Z= 0.133 Angle : 0.459 3.534 2084 Z= 0.241 Chirality : 0.046 0.132 244 Planarity : 0.005 0.034 263 Dihedral : 4.183 21.359 206 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % 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 (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: -0.81 (0.61), residues: 200 helix: -0.08 (0.52), residues: 93 sheet: 0.86 (1.28), residues: 22 loop : -1.39 (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 0.008 0.001 PHE A 196 TYR 0.003 0.001 TYR A 107 ARG 0.002 0.000 ARG A 17 *********************** 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 24 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.181 Fit side-chains REVERT: A 92 LEU cc_start: 0.8405 (mt) cc_final: 0.8138 (mm) REVERT: A 112 MET cc_start: 0.4743 (ttt) cc_final: 0.4335 (ttp) REVERT: A 144 MET cc_start: 0.7688 (ttp) cc_final: 0.7347 (ttm) REVERT: A 191 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7715 (tm-30) outliers start: 2 outliers final: 2 residues processed: 24 average time/residue: 0.1749 time to fit residues: 4.7978 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 : 0.183 ------------------------------------------------------------------------------- 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: 3.9990 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 12 optimal weight: 0.0030 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 0.0670 overall best weight: 0.5930 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.125309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.108084 restraints weight = 2025.217| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.84 r_work: 0.3382 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1545 Z= 0.127 Angle : 0.441 3.415 2084 Z= 0.229 Chirality : 0.046 0.125 244 Planarity : 0.005 0.036 263 Dihedral : 3.702 11.462 205 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % 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: -0.34 (0.62), residues: 200 helix: 0.24 (0.53), residues: 93 sheet: 1.10 (1.29), residues: 22 loop : -1.05 (0.73), residues: 85 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 0.008 0.001 PHE A 196 TYR 0.003 0.001 TYR A 107 ARG 0.001 0.000 ARG A 17 *********************** 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: 3 poor density : 22 time to evaluate : 0.188 Fit side-chains REVERT: A 112 MET cc_start: 0.5103 (ttt) cc_final: 0.4699 (ttp) REVERT: A 144 MET cc_start: 0.7636 (ttp) cc_final: 0.7358 (ttm) outliers start: 3 outliers final: 2 residues processed: 25 average time/residue: 0.1566 time to fit residues: 4.5192 Evaluate side-chains 19 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.184 ------------------------------------------------------------------------------- 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 11 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 0.1980 chunk 4 optimal weight: 0.4980 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3600 r_free = 0.3600 target = 0.120855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.101845 restraints weight = 1932.328| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.25 r_work: 0.3257 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 1545 Z= 0.156 Angle : 0.481 3.777 2084 Z= 0.251 Chirality : 0.046 0.122 244 Planarity : 0.005 0.037 263 Dihedral : 3.691 11.606 205 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % 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: -0.09 (0.62), residues: 200 helix: 0.40 (0.52), residues: 94 sheet: 1.18 (1.30), residues: 22 loop : -0.85 (0.75), residues: 84 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 0.007 0.001 PHE A 196 TYR 0.002 0.001 TYR A 107 ARG 0.001 0.000 ARG A 17 *********************** 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 26 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.197 Fit side-chains REVERT: A 92 LEU cc_start: 0.8362 (mt) cc_final: 0.8020 (mm) REVERT: A 112 MET cc_start: 0.4834 (ttt) cc_final: 0.4401 (ttp) REVERT: A 144 MET cc_start: 0.7614 (ttp) cc_final: 0.7312 (ttm) outliers start: 3 outliers final: 3 residues processed: 26 average time/residue: 0.1545 time to fit residues: 4.6585 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 : 0.184 ------------------------------------------------------------------------------- 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: 4.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 chunk 14 optimal weight: 0.0970 chunk 9 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3626 r_free = 0.3626 target = 0.121933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.103630 restraints weight = 1933.963| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.97 r_work: 0.3303 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 1545 Z= 0.144 Angle : 0.481 6.413 2084 Z= 0.249 Chirality : 0.046 0.122 244 Planarity : 0.005 0.036 263 Dihedral : 3.648 11.932 205 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % 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: 0.15 (0.62), residues: 200 helix: 0.61 (0.52), residues: 94 sheet: 1.21 (1.30), residues: 22 loop : -0.73 (0.76), residues: 84 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 0.007 0.001 PHE A 196 TYR 0.003 0.001 TYR A 107 ARG 0.001 0.000 ARG A 17 *********************** 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 : 0.193 Fit side-chains REVERT: A 92 LEU cc_start: 0.8333 (mt) cc_final: 0.8032 (mm) REVERT: A 112 MET cc_start: 0.4920 (ttt) cc_final: 0.4491 (ttp) REVERT: A 144 MET cc_start: 0.7601 (ttp) cc_final: 0.7329 (ttm) outliers start: 3 outliers final: 3 residues processed: 24 average time/residue: 0.1624 time to fit residues: 4.5367 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 : 0.177 ------------------------------------------------------------------------------- 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: 0.0770 chunk 15 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 overall best weight: 0.7340 ------------------------------------------------------------------------------- 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 = 0.3633 r_free = 0.3633 target = 0.122618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.103810 restraints weight = 2003.063| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.05 r_work: 0.3299 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 1545 Z= 0.145 Angle : 0.488 5.974 2084 Z= 0.253 Chirality : 0.046 0.121 244 Planarity : 0.005 0.035 263 Dihedral : 3.627 12.032 205 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.48 % Allowed : 18.63 % Favored : 78.88 % 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: 0.32 (0.63), residues: 200 helix: 0.81 (0.52), residues: 94 sheet: 1.25 (1.30), residues: 22 loop : -0.71 (0.77), 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 0.013 0.001 PHE A 99 TYR 0.003 0.001 TYR A 107 ARG 0.004 0.001 ARG A 77 *********************** 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 26 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.164 Fit side-chains REVERT: A 92 LEU cc_start: 0.8335 (mt) cc_final: 0.8031 (mm) REVERT: A 112 MET cc_start: 0.4925 (ttt) cc_final: 0.4495 (ttp) REVERT: A 144 MET cc_start: 0.7601 (ttp) cc_final: 0.7337 (ttm) outliers start: 4 outliers final: 4 residues processed: 25 average time/residue: 0.1403 time to fit residues: 4.0889 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 : 0.169 ------------------------------------------------------------------------------- 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 121 MET 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: 7.9990 chunk 18 optimal weight: 6.9990 chunk 13 optimal weight: 0.2980 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3633 r_free = 0.3633 target = 0.122719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.104105 restraints weight = 2004.536| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.03 r_work: 0.3302 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 1545 Z= 0.149 Angle : 0.489 5.956 2084 Z= 0.253 Chirality : 0.046 0.123 244 Planarity : 0.005 0.034 263 Dihedral : 3.638 12.544 205 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.48 % Allowed : 17.39 % 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: 0.32 (0.64), residues: 200 helix: 0.81 (0.52), residues: 95 sheet: 1.31 (1.31), residues: 22 loop : -0.73 (0.80), residues: 83 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 0.008 0.001 PHE A 196 TYR 0.005 0.001 TYR A 107 ARG 0.006 0.001 ARG A 77 ********************** 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 25 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.230 Fit side-chains REVERT: A 92 LEU cc_start: 0.8333 (mt) cc_final: 0.8026 (mm) REVERT: A 112 MET cc_start: 0.4959 (ttt) cc_final: 0.4529 (ttp) REVERT: A 144 MET cc_start: 0.7580 (ttp) cc_final: 0.7269 (ttm) outliers start: 4 outliers final: 4 residues processed: 24 average time/residue: 0.1636 time to fit residues: 4.5478 Evaluate side-chains 24 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.186 ------------------------------------------------------------------------------- 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 121 MET 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: 7.9990 chunk 4 optimal weight: 0.9980 chunk 9 optimal weight: 0.0030 chunk 11 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 14 optimal weight: 0.0870 chunk 13 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 3 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.5768 ------------------------------------------------------------------------------- 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 = 0.3650 r_free = 0.3650 target = 0.124301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.105761 restraints weight = 1997.843| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.03 r_work: 0.3324 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 1545 Z= 0.133 Angle : 0.470 6.035 2084 Z= 0.242 Chirality : 0.045 0.121 244 Planarity : 0.004 0.032 263 Dihedral : 3.477 11.359 205 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.11 % Allowed : 17.39 % 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: 0.51 (0.64), residues: 200 helix: 0.95 (0.51), residues: 95 sheet: 1.12 (1.13), residues: 27 loop : -0.64 (0.85), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 167 HIS 0.002 0.001 HIS A 10 PHE 0.008 0.001 PHE A 196 TYR 0.004 0.001 TYR A 107 ARG 0.001 0.000 ARG A 17 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1543.01 seconds wall clock time: 27 minutes 22.13 seconds (1642.13 seconds total)