Starting phenix.real_space_refine on Mon Sep 23 11:49:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wx4_32876/09_2024/7wx4_32876.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wx4_32876/09_2024/7wx4_32876.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wx4_32876/09_2024/7wx4_32876.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wx4_32876/09_2024/7wx4_32876.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wx4_32876/09_2024/7wx4_32876.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wx4_32876/09_2024/7wx4_32876.cif" } resolution = 3.4 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= 0.000 sd= 0.005 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 15 5.16 5 C 1256 2.51 5 N 339 2.21 5 O 382 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 1992 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1887 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 8, 'TRANS': 238} Chain breaks: 3 Chain: "E" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Time building chain proxies: 2.26, per 1000 atoms: 1.13 Number of scatterers: 1992 At special positions: 0 Unit cell: (71.02, 57.24, 81.62, 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 15 16.00 O 382 8.00 N 339 7.00 C 1256 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 - 3.00 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: 0.48 Conformation dependent library (CDL) restraints added in 254.2 milliseconds 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 488 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 2 sheets defined 48.5% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 64 through 69 removed outlier: 4.221A pdb=" N ILE A 68 " --> pdb=" O GLY A 64 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 64 through 69' Processing helix chain 'A' and resid 77 through 93 Processing helix chain 'A' and resid 104 through 119 removed outlier: 4.150A pdb=" N PHE A 108 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.601A pdb=" N LEU A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 163 Processing helix chain 'A' and resid 175 through 179 Processing helix chain 'A' and resid 180 through 197 removed outlier: 3.604A pdb=" N LEU A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 321 through 329 removed outlier: 3.751A pdb=" N THR A 325 " --> pdb=" O LYS A 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 121 removed outlier: 3.790A pdb=" N LEU E 121 " --> pdb=" O LEU E 118 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 63 removed outlier: 6.466A pdb=" N VAL A 60 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N MET A 252 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LYS A 62 " --> pdb=" O MET A 252 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 249 " --> pdb=" O SER A 311 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL A 312 " --> pdb=" O PHE A 336 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 168 through 173 removed outlier: 3.685A pdb=" N ALA A 169 " --> pdb=" O VAL A 200 " (cutoff:3.500A) 89 hydrogen bonds defined for protein. 255 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: 0.45 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 659 1.34 - 1.46: 304 1.46 - 1.57: 1026 1.57 - 1.69: 0 1.69 - 1.80: 27 Bond restraints: 2016 Sorted by residual: bond pdb=" CB VAL A 200 " pdb=" CG2 VAL A 200 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.07e+00 bond pdb=" CG1 ILE A 202 " pdb=" CD1 ILE A 202 " ideal model delta sigma weight residual 1.513 1.477 0.036 3.90e-02 6.57e+02 8.61e-01 bond pdb=" CB PHE A 108 " pdb=" CG PHE A 108 " ideal model delta sigma weight residual 1.502 1.481 0.021 2.30e-02 1.89e+03 8.22e-01 bond pdb=" CB ILE A 202 " pdb=" CG2 ILE A 202 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.93e-01 bond pdb=" CA ASN A 206 " pdb=" C ASN A 206 " ideal model delta sigma weight residual 1.526 1.516 0.010 1.15e-02 7.56e+03 7.87e-01 ... (remaining 2011 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.93: 2438 0.93 - 1.86: 243 1.86 - 2.79: 28 2.79 - 3.72: 7 3.72 - 4.65: 2 Bond angle restraints: 2718 Sorted by residual: angle pdb=" C MET A 271 " pdb=" N HIS A 272 " pdb=" CA HIS A 272 " ideal model delta sigma weight residual 121.54 125.37 -3.83 1.91e+00 2.74e-01 4.01e+00 angle pdb=" N MET A 123 " pdb=" CA MET A 123 " pdb=" C MET A 123 " ideal model delta sigma weight residual 113.01 110.65 2.36 1.20e+00 6.94e-01 3.86e+00 angle pdb=" C ILE A 202 " pdb=" N ILE A 203 " pdb=" CA ILE A 203 " ideal model delta sigma weight residual 120.34 123.35 -3.01 1.58e+00 4.01e-01 3.64e+00 angle pdb=" NE ARG A 96 " pdb=" CZ ARG A 96 " pdb=" NH1 ARG A 96 " ideal model delta sigma weight residual 121.50 119.73 1.77 1.00e+00 1.00e+00 3.14e+00 angle pdb=" C THR A 334 " pdb=" N PHE A 335 " pdb=" CA PHE A 335 " ideal model delta sigma weight residual 121.42 123.91 -2.49 1.43e+00 4.89e-01 3.04e+00 ... (remaining 2713 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 1072 17.55 - 35.09: 121 35.09 - 52.63: 40 52.63 - 70.18: 5 70.18 - 87.72: 3 Dihedral angle restraints: 1241 sinusoidal: 492 harmonic: 749 Sorted by residual: dihedral pdb=" CA LEU A 76 " pdb=" C LEU A 76 " pdb=" N ALA A 77 " pdb=" CA ALA A 77 " ideal model delta harmonic sigma weight residual 180.00 163.71 16.29 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CB GLU A 182 " pdb=" CG GLU A 182 " pdb=" CD GLU A 182 " pdb=" OE1 GLU A 182 " ideal model delta sinusoidal sigma weight residual 0.00 87.72 -87.72 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" N ASN A 260 " pdb=" CA ASN A 260 " pdb=" CB ASN A 260 " pdb=" CG ASN A 260 " ideal model delta sinusoidal sigma weight residual -180.00 -120.25 -59.75 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1238 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 164 0.027 - 0.054: 110 0.054 - 0.081: 28 0.081 - 0.108: 18 0.108 - 0.135: 5 Chirality restraints: 325 Sorted by residual: chirality pdb=" CA ILE A 199 " pdb=" N ILE A 199 " pdb=" C ILE A 199 " pdb=" CB ILE A 199 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA VAL A 101 " pdb=" N VAL A 101 " pdb=" C VAL A 101 " pdb=" CB VAL A 101 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CA ILE A 203 " pdb=" N ILE A 203 " pdb=" C ILE A 203 " pdb=" CB ILE A 203 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.38e-01 ... (remaining 322 not shown) Planarity restraints: 343 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 175 " -0.017 5.00e-02 4.00e+02 2.51e-02 1.01e+00 pdb=" N PRO A 176 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO A 176 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 176 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 335 " -0.009 2.00e-02 2.50e+03 7.55e-03 9.99e-01 pdb=" CG PHE A 335 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 PHE A 335 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 335 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 335 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 335 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 335 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 261 " 0.014 5.00e-02 4.00e+02 2.15e-02 7.39e-01 pdb=" N PRO A 262 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO A 262 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 262 " 0.012 5.00e-02 4.00e+02 ... (remaining 340 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 335 2.75 - 3.29: 1852 3.29 - 3.83: 3072 3.83 - 4.36: 3457 4.36 - 4.90: 6040 Nonbonded interactions: 14756 Sorted by model distance: nonbonded pdb=" OE2 GLU A 94 " pdb=" NH1 ARG A 96 " model vdw 2.219 3.120 nonbonded pdb=" O SER A 311 " pdb=" OG SER A 311 " model vdw 2.294 3.040 nonbonded pdb=" O SER E 120 " pdb=" OG SER E 120 " model vdw 2.296 3.040 nonbonded pdb=" OD1 ASP A 232 " pdb=" N SER A 235 " model vdw 2.342 3.120 nonbonded pdb=" N GLU A 49 " pdb=" OE1 GLN A 52 " model vdw 2.356 3.120 ... (remaining 14751 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.400 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.570 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 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 : 0.006 0.036 2016 Z= 0.363 Angle : 0.589 4.648 2718 Z= 0.346 Chirality : 0.042 0.135 325 Planarity : 0.003 0.025 343 Dihedral : 16.463 87.722 753 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 6.39 % Allowed : 21.00 % Favored : 72.60 % 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: -3.40 (0.48), residues: 250 helix: -0.47 (0.47), residues: 110 sheet: -5.04 (0.61), residues: 37 loop : -3.11 (0.47), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 304 HIS 0.002 0.001 HIS A 272 PHE 0.017 0.002 PHE A 335 TYR 0.005 0.001 TYR A 259 ARG 0.001 0.000 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 60 time to evaluate : 0.234 Fit side-chains REVERT: A 74 HIS cc_start: 0.6343 (OUTLIER) cc_final: 0.5656 (t70) REVERT: A 174 THR cc_start: 0.8561 (OUTLIER) cc_final: 0.8346 (p) REVERT: A 316 ASN cc_start: 0.7358 (t0) cc_final: 0.7120 (t0) REVERT: E 123 MET cc_start: 0.9138 (mmm) cc_final: 0.8166 (tpp) outliers start: 14 outliers final: 9 residues processed: 69 average time/residue: 0.1574 time to fit residues: 12.3296 Evaluate side-chains 64 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 53 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain E residue 116 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 0.0370 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN A 111 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2016 Z= 0.156 Angle : 0.467 4.957 2718 Z= 0.250 Chirality : 0.040 0.128 325 Planarity : 0.003 0.027 343 Dihedral : 7.792 55.379 290 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.57 % Allowed : 25.57 % Favored : 69.86 % 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: -2.12 (0.53), residues: 250 helix: 0.59 (0.51), residues: 117 sheet: -4.79 (0.61), residues: 37 loop : -2.45 (0.54), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 304 HIS 0.001 0.000 HIS A 92 PHE 0.014 0.002 PHE A 335 TYR 0.004 0.001 TYR A 157 ARG 0.004 0.000 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 0.236 Fit side-chains REVERT: A 90 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6614 (tp30) REVERT: A 306 LEU cc_start: 0.8585 (tp) cc_final: 0.8218 (tp) REVERT: E 123 MET cc_start: 0.9127 (mmm) cc_final: 0.8761 (tpp) outliers start: 10 outliers final: 9 residues processed: 62 average time/residue: 0.1054 time to fit residues: 7.8716 Evaluate side-chains 59 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 49 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 117 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 6 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 7 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 0.3980 chunk 15 optimal weight: 0.0980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2016 Z= 0.154 Angle : 0.457 4.929 2718 Z= 0.245 Chirality : 0.039 0.124 325 Planarity : 0.003 0.031 343 Dihedral : 6.064 55.755 279 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 5.94 % Allowed : 24.66 % Favored : 69.41 % 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: -1.43 (0.56), residues: 250 helix: 1.02 (0.52), residues: 118 sheet: -4.46 (0.59), residues: 37 loop : -1.95 (0.61), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 264 HIS 0.001 0.000 HIS A 272 PHE 0.010 0.001 PHE A 335 TYR 0.004 0.001 TYR A 259 ARG 0.003 0.000 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 52 time to evaluate : 0.169 Fit side-chains REVERT: A 90 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6627 (tp30) REVERT: A 193 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7167 (tm-30) REVERT: E 116 GLU cc_start: 0.5989 (OUTLIER) cc_final: 0.5583 (mt-10) REVERT: E 123 MET cc_start: 0.9058 (mmm) cc_final: 0.8809 (tpp) outliers start: 13 outliers final: 7 residues processed: 63 average time/residue: 0.1134 time to fit residues: 8.6595 Evaluate side-chains 60 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 51 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 117 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 11 optimal weight: 0.0170 chunk 21 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 20 optimal weight: 0.2980 chunk 13 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2016 Z= 0.131 Angle : 0.434 4.955 2718 Z= 0.231 Chirality : 0.039 0.145 325 Planarity : 0.004 0.041 343 Dihedral : 5.872 55.917 279 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 5.02 % Allowed : 26.03 % Favored : 68.95 % 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: -0.96 (0.56), residues: 250 helix: 1.31 (0.51), residues: 118 sheet: -4.20 (0.57), residues: 39 loop : -1.48 (0.66), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 264 HIS 0.000 0.000 HIS A 92 PHE 0.024 0.002 PHE A 188 TYR 0.004 0.001 TYR A 259 ARG 0.003 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 55 time to evaluate : 0.227 Fit side-chains REVERT: A 76 LEU cc_start: 0.8176 (mt) cc_final: 0.7879 (mt) REVERT: A 90 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6577 (tp30) REVERT: A 193 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7326 (tm-30) REVERT: A 265 GLU cc_start: 0.5270 (OUTLIER) cc_final: 0.4695 (mp0) REVERT: A 306 LEU cc_start: 0.8514 (tp) cc_final: 0.8240 (tp) REVERT: E 116 GLU cc_start: 0.6046 (OUTLIER) cc_final: 0.5753 (mt-10) REVERT: E 123 MET cc_start: 0.9017 (mmm) cc_final: 0.8778 (tpp) outliers start: 11 outliers final: 8 residues processed: 61 average time/residue: 0.1000 time to fit residues: 7.4524 Evaluate side-chains 66 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 55 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 117 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 0 optimal weight: 4.9990 chunk 12 optimal weight: 0.0670 chunk 21 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2016 Z= 0.201 Angle : 0.463 4.959 2718 Z= 0.245 Chirality : 0.040 0.148 325 Planarity : 0.003 0.028 343 Dihedral : 5.838 58.912 278 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 5.94 % Allowed : 27.40 % Favored : 66.67 % 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: -0.80 (0.56), residues: 250 helix: 1.37 (0.51), residues: 118 sheet: -4.10 (0.58), residues: 39 loop : -1.31 (0.66), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 264 HIS 0.001 0.000 HIS A 272 PHE 0.013 0.002 PHE A 335 TYR 0.006 0.001 TYR A 259 ARG 0.002 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 54 time to evaluate : 0.174 Fit side-chains REVERT: A 76 LEU cc_start: 0.8255 (mt) cc_final: 0.7944 (mt) REVERT: A 90 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6623 (tp30) REVERT: A 193 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7316 (tm-30) REVERT: A 265 GLU cc_start: 0.5300 (OUTLIER) cc_final: 0.4742 (mp0) REVERT: E 123 MET cc_start: 0.9023 (mmm) cc_final: 0.8803 (tpp) outliers start: 13 outliers final: 8 residues processed: 62 average time/residue: 0.0907 time to fit residues: 6.8047 Evaluate side-chains 64 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain E residue 117 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 0.0980 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2016 Z= 0.174 Angle : 0.448 5.001 2718 Z= 0.238 Chirality : 0.039 0.141 325 Planarity : 0.003 0.029 343 Dihedral : 4.388 40.538 275 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 5.94 % Allowed : 27.40 % Favored : 66.67 % 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: -0.63 (0.56), residues: 250 helix: 1.46 (0.51), residues: 118 sheet: -3.92 (0.58), residues: 39 loop : -1.18 (0.66), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 264 HIS 0.001 0.000 HIS A 92 PHE 0.012 0.001 PHE A 335 TYR 0.006 0.001 TYR A 259 ARG 0.002 0.000 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 55 time to evaluate : 0.224 Fit side-chains REVERT: A 76 LEU cc_start: 0.8207 (mt) cc_final: 0.7935 (mt) REVERT: A 90 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6681 (tp30) REVERT: A 193 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7322 (tm-30) REVERT: A 265 GLU cc_start: 0.5516 (OUTLIER) cc_final: 0.4501 (mp0) REVERT: E 123 MET cc_start: 0.9019 (mmm) cc_final: 0.8801 (tpp) outliers start: 13 outliers final: 11 residues processed: 63 average time/residue: 0.1077 time to fit residues: 8.2625 Evaluate side-chains 66 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 53 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 122 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 14 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 0.0050 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2016 Z= 0.196 Angle : 0.461 4.961 2718 Z= 0.245 Chirality : 0.039 0.143 325 Planarity : 0.003 0.029 343 Dihedral : 4.254 35.522 275 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 6.85 % Allowed : 26.94 % Favored : 66.21 % 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: -0.53 (0.56), residues: 250 helix: 1.46 (0.51), residues: 118 sheet: -3.82 (0.58), residues: 39 loop : -1.03 (0.67), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 264 HIS 0.001 0.000 HIS A 272 PHE 0.013 0.001 PHE A 335 TYR 0.006 0.001 TYR A 259 ARG 0.002 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 51 time to evaluate : 0.229 Fit side-chains REVERT: A 76 LEU cc_start: 0.8212 (mt) cc_final: 0.7955 (mt) REVERT: A 90 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.6858 (tp30) REVERT: A 193 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7323 (tm-30) REVERT: A 265 GLU cc_start: 0.5537 (OUTLIER) cc_final: 0.5012 (mp0) REVERT: E 123 MET cc_start: 0.9032 (mmm) cc_final: 0.8827 (tpp) outliers start: 15 outliers final: 11 residues processed: 61 average time/residue: 0.0999 time to fit residues: 7.4666 Evaluate side-chains 64 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 51 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 122 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2016 Z= 0.188 Angle : 0.460 4.956 2718 Z= 0.245 Chirality : 0.039 0.140 325 Planarity : 0.003 0.028 343 Dihedral : 4.185 33.304 275 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 5.94 % Allowed : 28.77 % Favored : 65.30 % 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: -0.43 (0.56), residues: 250 helix: 1.49 (0.51), residues: 118 sheet: -3.68 (0.59), residues: 39 loop : -0.95 (0.67), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 264 HIS 0.001 0.000 HIS A 272 PHE 0.013 0.001 PHE A 335 TYR 0.006 0.001 TYR A 259 ARG 0.001 0.000 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 53 time to evaluate : 0.222 Fit side-chains REVERT: A 76 LEU cc_start: 0.8207 (mt) cc_final: 0.7950 (mt) REVERT: A 90 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6861 (tp30) REVERT: A 193 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7334 (tm-30) REVERT: A 265 GLU cc_start: 0.5495 (OUTLIER) cc_final: 0.5005 (mp0) REVERT: E 123 MET cc_start: 0.9029 (mmm) cc_final: 0.8827 (tpp) outliers start: 13 outliers final: 10 residues processed: 62 average time/residue: 0.1064 time to fit residues: 7.9768 Evaluate side-chains 63 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 51 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 122 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 24 optimal weight: 0.0020 chunk 22 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 15 optimal weight: 0.0070 chunk 12 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.4606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2016 Z= 0.149 Angle : 0.460 5.074 2718 Z= 0.243 Chirality : 0.039 0.133 325 Planarity : 0.003 0.029 343 Dihedral : 3.967 31.008 275 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 5.48 % Allowed : 29.22 % Favored : 65.30 % 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: -0.20 (0.56), residues: 250 helix: 1.66 (0.51), residues: 118 sheet: -3.51 (0.58), residues: 39 loop : -0.83 (0.66), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 304 HIS 0.000 0.000 HIS A 92 PHE 0.009 0.001 PHE A 335 TYR 0.005 0.001 TYR A 179 ARG 0.001 0.000 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 56 time to evaluate : 0.241 Fit side-chains REVERT: A 90 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.6817 (tp30) REVERT: A 193 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7339 (tm-30) REVERT: A 265 GLU cc_start: 0.5543 (OUTLIER) cc_final: 0.4589 (mp0) outliers start: 12 outliers final: 10 residues processed: 65 average time/residue: 0.0994 time to fit residues: 7.9351 Evaluate side-chains 66 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 54 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 122 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 20 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 22 optimal weight: 0.2980 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2016 Z= 0.189 Angle : 0.488 4.948 2718 Z= 0.257 Chirality : 0.039 0.136 325 Planarity : 0.004 0.042 343 Dihedral : 4.002 31.070 275 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 5.02 % Allowed : 30.59 % Favored : 64.38 % 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: -0.17 (0.55), residues: 250 helix: 1.69 (0.51), residues: 118 sheet: -3.37 (0.60), residues: 39 loop : -0.89 (0.63), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 304 HIS 0.001 0.000 HIS A 272 PHE 0.012 0.001 PHE A 335 TYR 0.006 0.001 TYR A 259 ARG 0.003 0.000 ARG A 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 52 time to evaluate : 0.236 Fit side-chains REVERT: A 90 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6879 (tp30) REVERT: A 193 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7369 (tm-30) REVERT: A 265 GLU cc_start: 0.5643 (OUTLIER) cc_final: 0.4707 (mp0) REVERT: E 123 MET cc_start: 0.8902 (tpp) cc_final: 0.8449 (mmm) outliers start: 11 outliers final: 9 residues processed: 60 average time/residue: 0.0973 time to fit residues: 7.1761 Evaluate side-chains 63 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 52 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain E residue 117 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 10 optimal weight: 0.1980 chunk 2 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.164748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.124599 restraints weight = 2436.545| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.70 r_work: 0.3338 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2016 Z= 0.159 Angle : 0.465 4.930 2718 Z= 0.247 Chirality : 0.039 0.133 325 Planarity : 0.003 0.041 343 Dihedral : 3.878 30.562 275 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 5.48 % Allowed : 30.14 % Favored : 64.38 % 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: -0.01 (0.55), residues: 250 helix: 1.79 (0.51), residues: 118 sheet: -3.35 (0.56), residues: 42 loop : -0.62 (0.65), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 264 HIS 0.000 0.000 HIS A 272 PHE 0.010 0.001 PHE A 335 TYR 0.005 0.001 TYR A 259 ARG 0.003 0.000 ARG A 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 973.67 seconds wall clock time: 23 minutes 10.56 seconds (1390.56 seconds total)