Starting phenix.real_space_refine on Sun Mar 10 14:17:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vu8_32126/03_2024/7vu8_32126_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vu8_32126/03_2024/7vu8_32126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vu8_32126/03_2024/7vu8_32126.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vu8_32126/03_2024/7vu8_32126.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vu8_32126/03_2024/7vu8_32126_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vu8_32126/03_2024/7vu8_32126_updated.pdb" } resolution = 3.0 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= 0.001 sd= 0.006 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 5 5.16 5 C 914 2.51 5 N 251 2.21 5 O 262 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 62": "OD1" <-> "OD2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 99": "NH1" <-> "NH2" Residue "B TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 1433 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1433 Unusual residues: {'ACK': 1} Classifications: {'peptide': 170, 'undetermined': 1} Link IDs: {'PTRANS': 6, 'TRANS': 163, None: 1} Not linked: pdbres="GLU B 228 " pdbres="ACK B 301 " Time building chain proxies: 1.50, per 1000 atoms: 1.05 Number of scatterers: 1433 At special positions: 0 Unit cell: (66.066, 54.054, 48.048, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 5 16.00 P 1 15.00 O 262 8.00 N 251 7.00 C 914 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 0.62 Conformation dependent library (CDL) restraints added in 404.4 milliseconds 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 320 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 7 helices and 1 sheets defined 44.7% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'B' and resid 69 through 72 No H-bonds generated for 'chain 'B' and resid 69 through 72' Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.620A pdb=" N PHE B 83 " --> pdb=" O PHE B 79 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR B 86 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TYR B 87 " --> pdb=" O PHE B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 114 Processing helix chain 'B' and resid 130 through 145 removed outlier: 4.346A pdb=" N MET B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU B 138 " --> pdb=" O MET B 134 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 179 removed outlier: 3.683A pdb=" N LYS B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA B 178 " --> pdb=" O PHE B 174 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ASN B 179 " --> pdb=" O ARG B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 198 removed outlier: 4.061A pdb=" N LYS B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY B 197 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASP B 198 " --> pdb=" O LYS B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 226 removed outlier: 3.817A pdb=" N HIS B 224 " --> pdb=" O ASP B 220 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE B 225 " --> pdb=" O ILE B 221 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 63 through 66 removed outlier: 6.384A pdb=" N ILE B 117 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N SER B 66 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL B 119 " --> pdb=" O SER B 66 " (cutoff:3.500A) No H-bonds generated for sheet with id= A 33 hydrogen bonds defined for protein. 99 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: 0.27 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 341 1.33 - 1.45: 326 1.45 - 1.57: 796 1.57 - 1.69: 2 1.69 - 1.81: 7 Bond restraints: 1472 Sorted by residual: bond pdb=" O3P ACK B 301 " pdb=" P ACK B 301 " ideal model delta sigma weight residual 1.588 1.480 0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" C PHE B 76 " pdb=" O PHE B 76 " ideal model delta sigma weight residual 1.235 1.288 -0.054 1.23e-02 6.61e+03 1.89e+01 bond pdb=" C THR B 77 " pdb=" O THR B 77 " ideal model delta sigma weight residual 1.236 1.284 -0.047 1.25e-02 6.40e+03 1.43e+01 bond pdb=" N ILE B 89 " pdb=" CA ILE B 89 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.15e-02 7.56e+03 1.27e+01 bond pdb=" N THR B 72 " pdb=" CA THR B 72 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.22e-02 6.72e+03 1.06e+01 ... (remaining 1467 not shown) Histogram of bond angle deviations from ideal: 92.92 - 101.14: 3 101.14 - 109.35: 125 109.35 - 117.56: 939 117.56 - 125.77: 887 125.77 - 133.98: 33 Bond angle restraints: 1987 Sorted by residual: angle pdb=" N ASP B 198 " pdb=" CA ASP B 198 " pdb=" C ASP B 198 " ideal model delta sigma weight residual 114.56 107.84 6.72 1.27e+00 6.20e-01 2.80e+01 angle pdb=" N TYR B 87 " pdb=" CA TYR B 87 " pdb=" C TYR B 87 " ideal model delta sigma weight residual 113.02 107.90 5.12 1.20e+00 6.94e-01 1.82e+01 angle pdb=" C LEU B 98 " pdb=" CA LEU B 98 " pdb=" CB LEU B 98 " ideal model delta sigma weight residual 117.23 112.07 5.16 1.36e+00 5.41e-01 1.44e+01 angle pdb=" CA VAL B 63 " pdb=" C VAL B 63 " pdb=" O VAL B 63 " ideal model delta sigma weight residual 121.49 117.79 3.70 1.01e+00 9.80e-01 1.34e+01 angle pdb=" N ASP B 95 " pdb=" CA ASP B 95 " pdb=" C ASP B 95 " ideal model delta sigma weight residual 114.39 109.10 5.29 1.45e+00 4.76e-01 1.33e+01 ... (remaining 1982 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.13: 868 31.13 - 62.26: 25 62.26 - 93.39: 0 93.39 - 124.51: 2 124.51 - 155.64: 2 Dihedral angle restraints: 897 sinusoidal: 400 harmonic: 497 Sorted by residual: dihedral pdb=" C2' ACK B 301 " pdb=" O2' ACK B 301 " pdb=" P ACK B 301 " pdb=" O1P ACK B 301 " ideal model delta sinusoidal sigma weight residual 124.10 -80.26 -155.64 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" C3' ACK B 301 " pdb=" O3' ACK B 301 " pdb=" P ACK B 301 " pdb=" O1P ACK B 301 " ideal model delta sinusoidal sigma weight residual 234.46 79.07 155.39 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" C3' ACK B 301 " pdb=" O3' ACK B 301 " pdb=" P ACK B 301 " pdb=" O3P ACK B 301 " ideal model delta sinusoidal sigma weight residual 105.56 -157.87 -96.57 1 3.00e+01 1.11e-03 1.19e+01 ... (remaining 894 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 124 0.047 - 0.094: 51 0.094 - 0.141: 18 0.141 - 0.188: 5 0.188 - 0.236: 6 Chirality restraints: 204 Sorted by residual: chirality pdb=" CA LYS B 100 " pdb=" N LYS B 100 " pdb=" C LYS B 100 " pdb=" CB LYS B 100 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB ILE B 104 " pdb=" CA ILE B 104 " pdb=" CG1 ILE B 104 " pdb=" CG2 ILE B 104 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA ILE B 151 " pdb=" N ILE B 151 " pdb=" C ILE B 151 " pdb=" CB ILE B 151 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 201 not shown) Planarity restraints: 251 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 70 " -0.016 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C PRO B 70 " 0.057 2.00e-02 2.50e+03 pdb=" O PRO B 70 " -0.022 2.00e-02 2.50e+03 pdb=" N ASP B 71 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 71 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.19e+00 pdb=" C ASP B 71 " 0.035 2.00e-02 2.50e+03 pdb=" O ASP B 71 " -0.013 2.00e-02 2.50e+03 pdb=" N THR B 72 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 86 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.59e+00 pdb=" C TYR B 86 " 0.033 2.00e-02 2.50e+03 pdb=" O TYR B 86 " -0.012 2.00e-02 2.50e+03 pdb=" N TYR B 87 " -0.011 2.00e-02 2.50e+03 ... (remaining 248 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 407 2.83 - 3.34: 1297 3.34 - 3.86: 2131 3.86 - 4.38: 2513 4.38 - 4.90: 3977 Nonbonded interactions: 10325 Sorted by model distance: nonbonded pdb=" OD1 ASP B 182 " pdb=" N GLY B 183 " model vdw 2.308 2.520 nonbonded pdb=" OE2 GLU B 138 " pdb=" NH2 ARG B 141 " model vdw 2.308 2.520 nonbonded pdb=" CD2 LEU B 98 " pdb=" N ARG B 99 " model vdw 2.426 3.540 nonbonded pdb=" NE ARG B 164 " pdb=" O GLY B 197 " model vdw 2.428 2.520 nonbonded pdb=" O ALA B 219 " pdb=" OG SER B 223 " model vdw 2.436 2.440 ... (remaining 10320 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: 0.690 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: 0.010 Extract box with map and model: 3.330 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.550 Find NCS groups from input model: 0.030 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:10.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 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 : 0.009 0.108 1472 Z= 0.624 Angle : 1.189 10.589 1987 Z= 0.809 Chirality : 0.069 0.236 204 Planarity : 0.005 0.033 251 Dihedral : 16.690 155.641 577 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 4.64 % Allowed : 7.95 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.27 (0.46), residues: 168 helix: -3.13 (0.41), residues: 66 sheet: -5.55 (0.71), residues: 19 loop : -3.25 (0.52), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 202 HIS 0.003 0.001 HIS B 165 PHE 0.007 0.001 PHE B 83 TYR 0.007 0.001 TYR B 87 ARG 0.003 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.173 Fit side-chains REVERT: B 72 THR cc_start: 0.8243 (p) cc_final: 0.8016 (p) REVERT: B 86 TYR cc_start: 0.7721 (m-80) cc_final: 0.7138 (t80) REVERT: B 119 VAL cc_start: 0.8934 (t) cc_final: 0.8672 (m) outliers start: 7 outliers final: 0 residues processed: 49 average time/residue: 0.7848 time to fit residues: 39.3235 Evaluate side-chains 24 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 14 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 6 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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: 0.7283 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1472 Z= 0.133 Angle : 0.545 4.966 1987 Z= 0.271 Chirality : 0.045 0.127 204 Planarity : 0.003 0.024 251 Dihedral : 17.888 140.660 220 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.96 % Allowed : 18.54 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.35 (0.57), residues: 168 helix: -1.08 (0.55), residues: 71 sheet: -4.65 (0.90), residues: 19 loop : -2.64 (0.61), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 189 HIS 0.002 0.001 HIS B 165 PHE 0.013 0.001 PHE B 92 TYR 0.011 0.001 TYR B 156 ARG 0.001 0.000 ARG B 93 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 30 time to evaluate : 0.160 Fit side-chains REVERT: B 86 TYR cc_start: 0.7733 (m-80) cc_final: 0.7163 (t80) outliers start: 9 outliers final: 3 residues processed: 33 average time/residue: 0.7529 time to fit residues: 25.5262 Evaluate side-chains 26 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 218 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 4 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 11 optimal weight: 0.0980 chunk 8 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- 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: 0.7295 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 1472 Z= 0.108 Angle : 0.511 8.339 1987 Z= 0.247 Chirality : 0.044 0.128 204 Planarity : 0.004 0.058 251 Dihedral : 17.896 150.844 220 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 5.30 % Allowed : 20.53 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.31 (0.64), residues: 168 helix: 0.03 (0.62), residues: 72 sheet: -4.45 (0.93), residues: 21 loop : -2.17 (0.69), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 202 HIS 0.002 0.001 HIS B 177 PHE 0.007 0.001 PHE B 92 TYR 0.005 0.001 TYR B 118 ARG 0.001 0.000 ARG B 149 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 24 time to evaluate : 0.170 Fit side-chains REVERT: B 78 ASP cc_start: 0.8184 (m-30) cc_final: 0.7757 (t0) REVERT: B 86 TYR cc_start: 0.7753 (m-80) cc_final: 0.7132 (t80) REVERT: B 150 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8535 (pp) outliers start: 8 outliers final: 2 residues processed: 30 average time/residue: 0.7810 time to fit residues: 24.0506 Evaluate side-chains 22 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 19 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 199 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 15 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 8 optimal weight: 0.0770 chunk 14 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- 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: 0.7328 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 1472 Z= 0.105 Angle : 0.507 8.120 1987 Z= 0.238 Chirality : 0.043 0.128 204 Planarity : 0.004 0.049 251 Dihedral : 18.077 156.794 220 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 5.30 % Allowed : 20.53 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.91 (0.62), residues: 168 helix: 0.44 (0.60), residues: 73 sheet: -3.98 (1.02), residues: 19 loop : -2.25 (0.63), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 131 HIS 0.002 0.001 HIS B 177 PHE 0.005 0.001 PHE B 76 TYR 0.005 0.001 TYR B 118 ARG 0.006 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 24 time to evaluate : 0.181 Fit side-chains REVERT: B 78 ASP cc_start: 0.8285 (m-30) cc_final: 0.7796 (t0) REVERT: B 86 TYR cc_start: 0.7651 (m-80) cc_final: 0.7066 (t80) REVERT: B 130 LYS cc_start: 0.3057 (pttt) cc_final: 0.2086 (mttp) REVERT: B 150 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8546 (pp) REVERT: B 226 SER cc_start: 0.5505 (t) cc_final: 0.4864 (m) outliers start: 8 outliers final: 7 residues processed: 30 average time/residue: 0.7155 time to fit residues: 22.0974 Evaluate side-chains 29 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 21 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 199 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 0 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 3 optimal weight: 0.0980 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 1472 Z= 0.097 Angle : 0.466 6.485 1987 Z= 0.222 Chirality : 0.043 0.129 204 Planarity : 0.003 0.042 251 Dihedral : 18.266 161.308 220 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 5.96 % Allowed : 19.21 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.56 (0.63), residues: 168 helix: 0.89 (0.62), residues: 73 sheet: -3.81 (1.02), residues: 19 loop : -2.25 (0.61), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 202 HIS 0.001 0.000 HIS B 177 PHE 0.005 0.001 PHE B 76 TYR 0.004 0.001 TYR B 118 ARG 0.005 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 23 time to evaluate : 0.169 Fit side-chains REVERT: B 78 ASP cc_start: 0.8316 (m-30) cc_final: 0.7807 (t0) REVERT: B 86 TYR cc_start: 0.7612 (m-80) cc_final: 0.6951 (t80) REVERT: B 130 LYS cc_start: 0.2834 (pttt) cc_final: 0.2139 (mttp) REVERT: B 150 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8540 (pp) REVERT: B 226 SER cc_start: 0.5590 (t) cc_final: 0.4956 (m) outliers start: 9 outliers final: 5 residues processed: 29 average time/residue: 0.7476 time to fit residues: 22.2893 Evaluate side-chains 27 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 21 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 199 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 0.0170 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.6026 ------------------------------------------------------------------------------- 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: 0.7348 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 1472 Z= 0.153 Angle : 0.526 6.119 1987 Z= 0.257 Chirality : 0.044 0.128 204 Planarity : 0.003 0.040 251 Dihedral : 18.207 159.333 220 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 6.62 % Allowed : 19.87 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.59 (0.63), residues: 168 helix: 1.00 (0.63), residues: 72 sheet: -3.88 (0.97), residues: 19 loop : -2.36 (0.60), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 131 HIS 0.002 0.001 HIS B 165 PHE 0.006 0.001 PHE B 76 TYR 0.005 0.001 TYR B 118 ARG 0.004 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 23 time to evaluate : 0.171 Fit side-chains REVERT: B 78 ASP cc_start: 0.8357 (m-30) cc_final: 0.7848 (t0) REVERT: B 86 TYR cc_start: 0.7629 (m-80) cc_final: 0.6977 (t80) REVERT: B 130 LYS cc_start: 0.2450 (pttt) cc_final: 0.1638 (mttp) REVERT: B 134 MET cc_start: 0.7377 (ptm) cc_final: 0.7130 (ptp) REVERT: B 150 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8450 (pp) REVERT: B 226 SER cc_start: 0.5621 (t) cc_final: 0.4999 (m) outliers start: 10 outliers final: 7 residues processed: 30 average time/residue: 0.6660 time to fit residues: 20.6078 Evaluate side-chains 27 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 19 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 218 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 9 optimal weight: 0.2980 chunk 4 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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: 0.7363 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1472 Z= 0.164 Angle : 0.539 5.798 1987 Z= 0.266 Chirality : 0.044 0.130 204 Planarity : 0.003 0.039 251 Dihedral : 18.230 159.009 220 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 6.62 % Allowed : 19.87 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.53 (0.63), residues: 168 helix: 1.01 (0.62), residues: 72 sheet: -3.62 (0.95), residues: 19 loop : -2.35 (0.60), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 202 HIS 0.002 0.001 HIS B 165 PHE 0.006 0.001 PHE B 76 TYR 0.005 0.001 TYR B 170 ARG 0.004 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 22 time to evaluate : 0.169 Fit side-chains REVERT: B 78 ASP cc_start: 0.8446 (m-30) cc_final: 0.7873 (t0) REVERT: B 86 TYR cc_start: 0.7665 (m-80) cc_final: 0.6986 (t80) REVERT: B 130 LYS cc_start: 0.2581 (pttt) cc_final: 0.1741 (mttp) REVERT: B 134 MET cc_start: 0.7300 (ptm) cc_final: 0.7045 (ptp) REVERT: B 150 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8427 (pp) REVERT: B 176 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7736 (ptpt) REVERT: B 226 SER cc_start: 0.5631 (t) cc_final: 0.5033 (m) outliers start: 10 outliers final: 6 residues processed: 30 average time/residue: 0.9000 time to fit residues: 27.5661 Evaluate side-chains 26 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 18 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 199 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 11 optimal weight: 0.0370 chunk 4 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 0.0020 chunk 16 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 overall best weight: 1.1870 ------------------------------------------------------------------------------- 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: 0.7342 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 1472 Z= 0.127 Angle : 0.534 5.573 1987 Z= 0.263 Chirality : 0.043 0.130 204 Planarity : 0.003 0.037 251 Dihedral : 18.292 161.201 220 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.31 % Allowed : 23.84 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.63), residues: 168 helix: 1.14 (0.62), residues: 72 sheet: -3.44 (0.98), residues: 21 loop : -2.19 (0.61), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 202 HIS 0.002 0.001 HIS B 165 PHE 0.006 0.001 PHE B 76 TYR 0.004 0.001 TYR B 118 ARG 0.004 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 25 time to evaluate : 0.169 Fit side-chains REVERT: B 78 ASP cc_start: 0.8374 (m-30) cc_final: 0.7831 (t0) REVERT: B 86 TYR cc_start: 0.7523 (m-80) cc_final: 0.6872 (t80) REVERT: B 130 LYS cc_start: 0.2437 (pttt) cc_final: 0.1678 (mttp) REVERT: B 134 MET cc_start: 0.7260 (ptm) cc_final: 0.7018 (ptp) REVERT: B 150 ILE cc_start: 0.8809 (pt) cc_final: 0.8423 (pp) REVERT: B 209 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8106 (mp0) REVERT: B 226 SER cc_start: 0.5594 (t) cc_final: 0.5011 (m) outliers start: 5 outliers final: 5 residues processed: 29 average time/residue: 0.8756 time to fit residues: 25.9989 Evaluate side-chains 26 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 21 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 199 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 12 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 3 optimal weight: 20.0000 chunk 13 optimal weight: 0.8980 chunk 5 optimal weight: 0.0870 chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 0 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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: 0.7305 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 1472 Z= 0.110 Angle : 0.526 5.667 1987 Z= 0.257 Chirality : 0.042 0.129 204 Planarity : 0.003 0.035 251 Dihedral : 18.353 163.629 220 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.32 % Allowed : 27.81 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.07 (0.64), residues: 168 helix: 1.27 (0.63), residues: 72 sheet: -2.90 (1.10), residues: 21 loop : -2.08 (0.63), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 202 HIS 0.001 0.000 HIS B 203 PHE 0.004 0.001 PHE B 64 TYR 0.004 0.001 TYR B 118 ARG 0.004 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 21 time to evaluate : 0.170 Fit side-chains REVERT: B 78 ASP cc_start: 0.8368 (m-30) cc_final: 0.7773 (t0) REVERT: B 86 TYR cc_start: 0.7519 (m-80) cc_final: 0.6909 (t80) REVERT: B 130 LYS cc_start: 0.2671 (pttt) cc_final: 0.2175 (mttp) REVERT: B 150 ILE cc_start: 0.8766 (pt) cc_final: 0.8396 (pp) REVERT: B 209 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8110 (mp0) REVERT: B 226 SER cc_start: 0.5570 (t) cc_final: 0.4992 (m) outliers start: 2 outliers final: 2 residues processed: 23 average time/residue: 0.6489 time to fit residues: 15.4804 Evaluate side-chains 21 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 19 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 129 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 9 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 16 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 2 optimal weight: 0.1980 chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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: 0.7352 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 1472 Z= 0.146 Angle : 0.536 5.058 1987 Z= 0.268 Chirality : 0.043 0.131 204 Planarity : 0.005 0.068 251 Dihedral : 18.194 159.154 220 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.32 % Allowed : 28.48 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.01 (0.64), residues: 168 helix: 1.32 (0.63), residues: 72 sheet: -2.94 (1.10), residues: 21 loop : -2.01 (0.63), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 202 HIS 0.002 0.001 HIS B 165 PHE 0.006 0.001 PHE B 76 TYR 0.016 0.001 TYR B 81 ARG 0.003 0.000 ARG B 141 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 19 time to evaluate : 0.171 Fit side-chains REVERT: B 78 ASP cc_start: 0.8422 (m-30) cc_final: 0.7845 (t0) REVERT: B 86 TYR cc_start: 0.7531 (m-80) cc_final: 0.6817 (t80) REVERT: B 130 LYS cc_start: 0.2680 (pttt) cc_final: 0.2105 (mttp) REVERT: B 150 ILE cc_start: 0.8791 (pt) cc_final: 0.8404 (pp) REVERT: B 209 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8166 (mp0) REVERT: B 226 SER cc_start: 0.5549 (t) cc_final: 0.5032 (m) outliers start: 2 outliers final: 2 residues processed: 21 average time/residue: 0.7335 time to fit residues: 16.0779 Evaluate side-chains 20 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 18 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 129 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 1 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 5 optimal weight: 8.9990 chunk 8 optimal weight: 0.1980 chunk 0 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.4050 r_free = 0.4050 target = 0.144846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.116579 restraints weight = 2297.819| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 4.69 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 1472 Z= 0.120 Angle : 0.523 5.146 1987 Z= 0.259 Chirality : 0.042 0.129 204 Planarity : 0.005 0.066 251 Dihedral : 18.291 161.706 220 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.32 % Allowed : 28.48 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.04 (0.64), residues: 168 helix: 1.32 (0.62), residues: 72 sheet: -2.91 (1.09), residues: 21 loop : -2.07 (0.63), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 202 HIS 0.001 0.000 HIS B 177 PHE 0.004 0.001 PHE B 67 TYR 0.014 0.001 TYR B 81 ARG 0.003 0.000 ARG B 141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1004.13 seconds wall clock time: 18 minutes 57.84 seconds (1137.84 seconds total)