Starting phenix.real_space_refine on Wed Nov 13 22:56:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jgc_36230/11_2024/8jgc_36230.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jgc_36230/11_2024/8jgc_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jgc_36230/11_2024/8jgc_36230.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jgc_36230/11_2024/8jgc_36230.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jgc_36230/11_2024/8jgc_36230.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jgc_36230/11_2024/8jgc_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-5513/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: 3.66, per 1000 atoms: 2.41 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: 0.39 Conformation dependent library (CDL) restraints added in 193.9 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: 0.35 Time building geometry restraints manager: 0.44 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: 6.550 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 11.320 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.530 ------------------------------------------------------------------------------- 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 : 0.188 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: 0.1246 time to fit residues: 4.1491 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 : 0.186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 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 1545 Z= 0.160 Angle : 0.533 3.708 2084 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 *********************** 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 : 0.175 Fit side-chains REVERT: A 17 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.7070 (mtm-85) REVERT: A 112 MET cc_start: 0.4716 (ttt) cc_final: 0.4382 (ttp) REVERT: A 144 MET cc_start: 0.7401 (ttp) cc_final: 0.7050 (ttm) outliers start: 6 outliers final: 3 residues processed: 33 average time/residue: 0.1239 time to fit residues: 4.7896 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 ------------------------------------------------------------------------------- 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 16 optimal weight: 0.0970 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 1545 Z= 0.150 Angle : 0.510 3.516 2084 Z= 0.269 Chirality : 0.048 0.147 244 Planarity : 0.005 0.036 263 Dihedral : 7.115 50.970 212 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.86 % Allowed : 12.42 % Favored : 85.71 % 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: -1.34 (0.61), residues: 200 helix: -0.44 (0.52), residues: 93 sheet: 0.82 (1.30), residues: 22 loop : -1.84 (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 0.010 0.001 PHE A 196 TYR 0.003 0.001 TYR A 107 ARG 0.001 0.000 ARG A 77 *********************** 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: 3 poor density : 23 time to evaluate : 0.177 Fit side-chains REVERT: A 17 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.5911 (mtp180) REVERT: A 112 MET cc_start: 0.4802 (ttt) cc_final: 0.4575 (ttp) REVERT: A 144 MET cc_start: 0.7238 (ttp) cc_final: 0.6986 (ttm) outliers start: 3 outliers final: 2 residues processed: 25 average time/residue: 0.1685 time to fit residues: 4.8138 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 : 0.189 ------------------------------------------------------------------------------- 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 9 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 14 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 1545 Z= 0.242 Angle : 0.554 3.740 2084 Z= 0.288 Chirality : 0.050 0.140 244 Planarity : 0.005 0.037 263 Dihedral : 6.321 45.385 210 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.48 % Allowed : 13.66 % 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: -1.42 (0.61), residues: 200 helix: -0.40 (0.52), residues: 93 sheet: 0.62 (1.28), residues: 22 loop : -1.96 (0.71), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 0.001 0.000 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 25 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.180 Fit side-chains REVERT: A 112 MET cc_start: 0.4862 (ttt) cc_final: 0.4581 (ttp) REVERT: A 144 MET cc_start: 0.7403 (ttp) cc_final: 0.7095 (ttm) outliers start: 4 outliers final: 3 residues processed: 24 average time/residue: 0.1528 time to fit residues: 4.2528 Evaluate side-chains 19 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 16 time to evaluate : 0.148 ------------------------------------------------------------------------------- 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 17 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 16 optimal weight: 0.0980 chunk 8 optimal weight: 5.9990 chunk 1 optimal weight: 0.0030 chunk 6 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.2244 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= 0.138 Angle : 0.465 3.547 2084 Z= 0.243 Chirality : 0.046 0.132 244 Planarity : 0.005 0.034 263 Dihedral : 4.176 20.666 206 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.24 % Allowed : 14.29 % 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: -0.81 (0.61), residues: 200 helix: -0.02 (0.52), residues: 93 sheet: 0.97 (1.30), residues: 22 loop : -1.50 (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 57 TYR 0.003 0.001 TYR A 107 ARG 0.001 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 20 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.183 Fit side-chains REVERT: A 112 MET cc_start: 0.4716 (ttt) cc_final: 0.4440 (ttp) REVERT: A 144 MET cc_start: 0.7307 (ttp) cc_final: 0.7055 (ttm) outliers start: 2 outliers final: 2 residues processed: 20 average time/residue: 0.1102 time to fit residues: 2.7234 Evaluate side-chains 17 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.142 ------------------------------------------------------------------------------- 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 2 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 3 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 1545 Z= 0.158 Angle : 0.467 3.493 2084 Z= 0.242 Chirality : 0.047 0.130 244 Planarity : 0.005 0.036 263 Dihedral : 3.876 12.555 205 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % 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: -0.58 (0.61), residues: 200 helix: 0.17 (0.52), residues: 93 sheet: 1.01 (1.30), residues: 22 loop : -1.35 (0.72), 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 0.004 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 22 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.178 Fit side-chains REVERT: A 112 MET cc_start: 0.4792 (ttt) cc_final: 0.4499 (ttp) REVERT: A 144 MET cc_start: 0.7343 (ttp) cc_final: 0.7094 (ttm) outliers start: 3 outliers final: 2 residues processed: 22 average time/residue: 0.1024 time to fit residues: 2.8076 Evaluate side-chains 17 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.176 ------------------------------------------------------------------------------- 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 3 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 9 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 18 optimal weight: 0.2980 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.2607 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= 0.159 Angle : 0.478 3.421 2084 Z= 0.249 Chirality : 0.046 0.128 244 Planarity : 0.005 0.036 263 Dihedral : 3.755 11.728 205 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.81 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: -0.29 (0.62), residues: 200 helix: 0.35 (0.52), residues: 93 sheet: 1.14 (1.31), residues: 22 loop : -1.13 (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 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 23 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.182 Fit side-chains REVERT: A 112 MET cc_start: 0.4720 (ttt) cc_final: 0.4431 (ttp) REVERT: A 144 MET cc_start: 0.7236 (ttp) cc_final: 0.7020 (ttm) outliers start: 2 outliers final: 2 residues processed: 23 average time/residue: 0.1118 time to fit residues: 3.1650 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 : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 185 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 14 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 0.0270 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 0.0970 chunk 1 optimal weight: 1.9990 overall best weight: 1.0240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 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 0.021 1545 Z= 0.160 Angle : 0.475 4.435 2084 Z= 0.246 Chirality : 0.046 0.123 244 Planarity : 0.005 0.036 263 Dihedral : 3.789 12.652 205 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.24 % Allowed : 18.01 % 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: -0.21 (0.61), residues: 200 helix: 0.40 (0.52), residues: 94 sheet: 1.07 (1.30), residues: 22 loop : -1.04 (0.74), 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 0.007 0.001 PHE A 57 TYR 0.002 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 22 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.194 Fit side-chains REVERT: A 112 MET cc_start: 0.4724 (ttt) cc_final: 0.4425 (ttp) REVERT: A 144 MET cc_start: 0.7265 (ttp) cc_final: 0.7015 (ttm) outliers start: 2 outliers final: 2 residues processed: 22 average time/residue: 0.1111 time to fit residues: 3.0463 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 : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 185 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 16 optimal weight: 0.0570 chunk 4 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 15 optimal weight: 0.2980 chunk 6 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 0.6980 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.2801 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= 0.145 Angle : 0.474 6.248 2084 Z= 0.246 Chirality : 0.046 0.126 244 Planarity : 0.005 0.034 263 Dihedral : 3.654 11.733 205 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % 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: 0.08 (0.62), residues: 200 helix: 0.63 (0.52), residues: 94 sheet: 1.15 (1.30), residues: 22 loop : -0.86 (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 0.008 0.001 PHE A 196 TYR 0.002 0.001 TYR A 107 ARG 0.001 0.000 ARG A 17 *********************** 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 22 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.192 Fit side-chains REVERT: A 112 MET cc_start: 0.4677 (ttt) cc_final: 0.4394 (ttp) REVERT: A 144 MET cc_start: 0.7219 (ttp) cc_final: 0.6972 (ttm) outliers start: 3 outliers final: 3 residues processed: 22 average time/residue: 0.1212 time to fit residues: 3.2777 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 : 0.190 ------------------------------------------------------------------------------- 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 18 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2881 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= 0.146 Angle : 0.475 6.039 2084 Z= 0.245 Chirality : 0.046 0.127 244 Planarity : 0.004 0.033 263 Dihedral : 3.636 12.175 205 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % 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: 0.14 (0.63), residues: 200 helix: 0.70 (0.52), residues: 95 sheet: 1.12 (1.30), residues: 22 loop : -0.86 (0.77), 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 0.003 0.001 TYR A 107 ARG 0.001 0.000 ARG A 17 ********************** 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 22 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.175 Fit side-chains REVERT: A 112 MET cc_start: 0.4650 (ttt) cc_final: 0.4328 (ttp) REVERT: A 144 MET cc_start: 0.7215 (ttp) cc_final: 0.6973 (ttm) outliers start: 3 outliers final: 3 residues processed: 22 average time/residue: 0.0634 time to fit residues: 1.9418 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 : 0.161 ------------------------------------------------------------------------------- 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 16 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.3609 r_free = 0.3609 target = 0.120764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.102261 restraints weight = 2015.222| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.04 r_work: 0.3274 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1545 Z= 0.203 Angle : 0.535 5.997 2084 Z= 0.273 Chirality : 0.048 0.132 244 Planarity : 0.005 0.034 263 Dihedral : 3.924 14.233 205 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % 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: -0.09 (0.61), residues: 200 helix: 0.54 (0.51), residues: 95 sheet: 0.91 (1.30), residues: 22 loop : -0.96 (0.75), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 167 HIS 0.003 0.001 HIS A 10 PHE 0.009 0.002 PHE A 57 TYR 0.005 0.002 TYR A 107 ARG 0.006 0.001 ARG A 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1163.20 seconds wall clock time: 23 minutes 1.84 seconds (1381.84 seconds total)