Starting phenix.real_space_refine on Sun Mar 10 14:27:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wx4_32876/03_2024/7wx4_32876.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wx4_32876/03_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_32876/03_2024/7wx4_32876.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wx4_32876/03_2024/7wx4_32876.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wx4_32876/03_2024/7wx4_32876.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wx4_32876/03_2024/7wx4_32876.pdb" } 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 Residue "A ARG 57": "NH1" <-> "NH2" Residue "A ARG 96": "NH1" <-> "NH2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A ARG 184": "NH1" <-> "NH2" Residue "A ASP 247": "OD1" <-> "OD2" Residue "A GLU 265": "OE1" <-> "OE2" Residue "A ARG 308": "NH1" <-> "NH2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "E GLU 116": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 1.65, per 1000 atoms: 0.83 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 - 3.50 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: 0.79 Conformation dependent library (CDL) restraints added in 384.2 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: 0.22 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: 0.46 Time building geometry restraints manager: 0.83 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: 99.36 - 106.28: 51 106.28 - 113.19: 1148 113.19 - 120.10: 690 120.10 - 127.01: 816 127.01 - 133.92: 13 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 2.520 nonbonded pdb=" O SER A 311 " pdb=" OG SER A 311 " model vdw 2.294 2.440 nonbonded pdb=" O SER E 120 " pdb=" OG SER E 120 " model vdw 2.296 2.440 nonbonded pdb=" OD1 ASP A 232 " pdb=" N SER A 235 " model vdw 2.342 2.520 nonbonded pdb=" N GLU A 49 " pdb=" OE1 GLN A 52 " model vdw 2.356 2.520 ... (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 ========== 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: 1.040 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: 4.980 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 10.470 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.000 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.420 ------------------------------------------------------------------------------- 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 : 0.193 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: 0.1404 time to fit residues: 11.0425 Evaluate side-chains 64 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 53 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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: 0.9980 chunk 18 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 0.0870 chunk 14 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 A 233 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1276 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= 0.166 Angle : 0.450 4.918 2718 Z= 0.241 Chirality : 0.039 0.127 325 Planarity : 0.003 0.027 343 Dihedral : 7.827 55.559 290 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 5.48 % Allowed : 26.03 % Favored : 68.49 % 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: -2.02 (0.53), residues: 250 helix: 0.89 (0.53), residues: 111 sheet: -4.79 (0.62), residues: 37 loop : -2.51 (0.52), residues: 102 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 0.014 0.002 PHE A 335 TYR 0.005 0.001 TYR A 157 ARG 0.005 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 68 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 56 time to evaluate : 0.268 Fit side-chains REVERT: A 58 ARG cc_start: 0.8400 (ttm170) cc_final: 0.8006 (mtm180) REVERT: A 90 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6620 (tp30) REVERT: A 306 LEU cc_start: 0.8558 (tp) cc_final: 0.8185 (tp) REVERT: A 316 ASN cc_start: 0.7308 (t0) cc_final: 0.7101 (t0) REVERT: E 123 MET cc_start: 0.9130 (mmm) cc_final: 0.7852 (tpp) outliers start: 12 outliers final: 9 residues processed: 65 average time/residue: 0.1498 time to fit residues: 11.4192 Evaluate side-chains 61 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 51 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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 106 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 256 ASP 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: 1.9990 chunk 22 optimal weight: 0.3980 chunk 24 optimal weight: 0.5980 chunk 20 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.1680 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= 0.158 Angle : 0.446 4.886 2718 Z= 0.236 Chirality : 0.039 0.125 325 Planarity : 0.003 0.028 343 Dihedral : 6.036 56.657 280 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 5.94 % Allowed : 25.57 % Favored : 68.49 % 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: -1.47 (0.56), residues: 250 helix: 1.04 (0.52), residues: 118 sheet: -4.55 (0.58), residues: 37 loop : -2.00 (0.62), 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 0.002 0.000 ARG A 330 *********************** 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 64 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 51 time to evaluate : 0.240 Fit side-chains REVERT: A 58 ARG cc_start: 0.8394 (ttm170) cc_final: 0.7998 (mtm180) REVERT: A 90 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6581 (tp30) REVERT: A 193 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7190 (tm-30) REVERT: A 316 ASN cc_start: 0.7487 (t0) cc_final: 0.7274 (t0) REVERT: E 116 GLU cc_start: 0.5947 (OUTLIER) cc_final: 0.5662 (mt-10) REVERT: E 123 MET cc_start: 0.9056 (mmm) cc_final: 0.7833 (tpp) outliers start: 13 outliers final: 7 residues processed: 62 average time/residue: 0.1132 time to fit residues: 8.3796 Evaluate side-chains 60 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 51 time to evaluate : 0.233 ------------------------------------------------------------------------------- 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 106 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 256 ASP 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: 0.4980 chunk 24 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7811 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2016 Z= 0.171 Angle : 0.440 4.874 2718 Z= 0.232 Chirality : 0.039 0.152 325 Planarity : 0.003 0.028 343 Dihedral : 5.362 58.982 278 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 5.02 % Allowed : 28.77 % 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: -1.14 (0.56), residues: 250 helix: 1.27 (0.52), residues: 118 sheet: -4.38 (0.55), residues: 39 loop : -1.70 (0.64), 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 0.005 0.001 TYR A 259 ARG 0.002 0.000 ARG A 50 *********************** 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 64 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 53 time to evaluate : 0.294 Fit side-chains REVERT: A 58 ARG cc_start: 0.8412 (ttm170) cc_final: 0.8006 (mtm180) REVERT: A 90 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6639 (tp30) REVERT: A 193 GLU cc_start: 0.8279 (tm-30) cc_final: 0.7333 (tm-30) REVERT: A 265 GLU cc_start: 0.5244 (OUTLIER) cc_final: 0.4683 (mp0) REVERT: E 123 MET cc_start: 0.9041 (mmm) cc_final: 0.7849 (tpp) outliers start: 11 outliers final: 8 residues processed: 59 average time/residue: 0.1111 time to fit residues: 7.8234 Evaluate side-chains 62 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 52 time to evaluate : 0.204 ------------------------------------------------------------------------------- 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 203 ILE Chi-restraints excluded: chain A residue 256 ASP 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 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: 0.7980 chunk 21 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 20 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN A 233 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2016 Z= 0.210 Angle : 0.462 4.891 2718 Z= 0.241 Chirality : 0.040 0.149 325 Planarity : 0.003 0.028 343 Dihedral : 4.025 25.099 275 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 6.85 % Allowed : 28.31 % Favored : 64.84 % 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: -1.00 (0.56), residues: 250 helix: 1.37 (0.51), residues: 119 sheet: -4.21 (0.56), residues: 39 loop : -1.68 (0.65), residues: 92 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 0.024 0.002 PHE A 188 TYR 0.005 0.001 TYR A 259 ARG 0.002 0.000 ARG A 50 *********************** 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 65 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 50 time to evaluate : 0.247 Fit side-chains REVERT: A 58 ARG cc_start: 0.8410 (ttm170) cc_final: 0.7965 (mtm180) REVERT: A 90 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6634 (tp30) REVERT: A 193 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7315 (tm-30) REVERT: A 265 GLU cc_start: 0.5288 (OUTLIER) cc_final: 0.4747 (mp0) REVERT: E 123 MET cc_start: 0.9088 (mmm) cc_final: 0.7980 (tpp) outliers start: 15 outliers final: 11 residues processed: 59 average time/residue: 0.1187 time to fit residues: 8.4300 Evaluate side-chains 63 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 50 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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 100 MET Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 256 ASP 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 116 GLU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 122 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 0.0030 chunk 13 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- 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: 0.7811 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2016 Z= 0.175 Angle : 0.445 4.875 2718 Z= 0.234 Chirality : 0.039 0.143 325 Planarity : 0.003 0.029 343 Dihedral : 3.921 23.916 275 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 7.76 % Allowed : 27.85 % 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: -0.67 (0.57), residues: 250 helix: 1.54 (0.52), residues: 118 sheet: -4.04 (0.58), residues: 39 loop : -1.34 (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 0.012 0.001 PHE A 335 TYR 0.005 0.001 TYR A 259 ARG 0.001 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 71 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 54 time to evaluate : 0.224 Fit side-chains REVERT: A 58 ARG cc_start: 0.8404 (ttm170) cc_final: 0.7945 (mtm180) REVERT: A 74 HIS cc_start: 0.6431 (OUTLIER) cc_final: 0.5714 (t70) REVERT: A 90 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6639 (tp30) REVERT: A 193 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7309 (tm-30) REVERT: A 265 GLU cc_start: 0.5376 (OUTLIER) cc_final: 0.4339 (mp0) REVERT: E 123 MET cc_start: 0.9062 (mmm) cc_final: 0.8786 (tpp) outliers start: 17 outliers final: 11 residues processed: 65 average time/residue: 0.1216 time to fit residues: 9.2939 Evaluate side-chains 66 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 52 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS 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 256 ASP Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 275 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 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: 0.6980 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 23 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 A 233 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2016 Z= 0.192 Angle : 0.455 4.791 2718 Z= 0.241 Chirality : 0.039 0.141 325 Planarity : 0.003 0.030 343 Dihedral : 3.922 23.901 275 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 6.85 % Allowed : 29.68 % Favored : 63.47 % 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: -0.67 (0.57), residues: 250 helix: 1.53 (0.51), residues: 118 sheet: -4.02 (0.58), residues: 39 loop : -1.33 (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 0.010 0.001 PHE A 335 TYR 0.006 0.001 TYR A 259 ARG 0.001 0.000 ARG A 50 *********************** 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 : 0.246 Fit side-chains REVERT: A 58 ARG cc_start: 0.8389 (ttm170) cc_final: 0.7934 (mtm180) REVERT: A 74 HIS cc_start: 0.6432 (OUTLIER) cc_final: 0.5713 (t70) REVERT: A 90 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6845 (tp30) REVERT: A 193 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7316 (tm-30) REVERT: A 265 GLU cc_start: 0.5392 (OUTLIER) cc_final: 0.4361 (mp0) REVERT: E 123 MET cc_start: 0.9093 (mmm) cc_final: 0.8837 (tpp) outliers start: 15 outliers final: 12 residues processed: 60 average time/residue: 0.1254 time to fit residues: 8.8946 Evaluate side-chains 66 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 51 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS 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 100 MET Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 175 LYS 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 116 GLU 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: 0.9990 chunk 23 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN A 233 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2165 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= 0.190 Angle : 0.457 4.788 2718 Z= 0.242 Chirality : 0.039 0.138 325 Planarity : 0.003 0.029 343 Dihedral : 3.896 23.395 275 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 8.22 % Allowed : 27.85 % Favored : 63.93 % 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: -0.59 (0.57), residues: 250 helix: 1.56 (0.51), residues: 118 sheet: -3.83 (0.60), residues: 39 loop : -1.31 (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 0.010 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 68 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 50 time to evaluate : 0.241 Fit side-chains REVERT: A 58 ARG cc_start: 0.8396 (ttm170) cc_final: 0.8119 (mtm180) REVERT: A 74 HIS cc_start: 0.6429 (OUTLIER) cc_final: 0.5711 (t70) REVERT: A 90 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.6850 (tp30) REVERT: A 193 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7336 (tm-30) REVERT: A 265 GLU cc_start: 0.5406 (OUTLIER) cc_final: 0.4381 (mp0) REVERT: E 123 MET cc_start: 0.9092 (mmm) cc_final: 0.8840 (tpp) outliers start: 18 outliers final: 14 residues processed: 62 average time/residue: 0.1243 time to fit residues: 9.1536 Evaluate side-chains 67 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 50 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS 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 100 MET Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 275 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 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: 6.9990 chunk 22 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 0.0050 chunk 15 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- 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: 0.7800 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2016 Z= 0.180 Angle : 0.455 4.771 2718 Z= 0.242 Chirality : 0.039 0.137 325 Planarity : 0.003 0.029 343 Dihedral : 3.849 22.251 275 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 6.85 % Allowed : 29.22 % Favored : 63.93 % 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: -0.49 (0.57), residues: 250 helix: 1.60 (0.51), residues: 118 sheet: -3.66 (0.62), residues: 39 loop : -1.26 (0.68), 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 0.010 0.001 PHE A 335 TYR 0.006 0.001 TYR A 259 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 66 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 51 time to evaluate : 0.248 Fit side-chains REVERT: A 58 ARG cc_start: 0.8412 (ttm170) cc_final: 0.8096 (mtm180) REVERT: A 74 HIS cc_start: 0.6424 (OUTLIER) cc_final: 0.5708 (t70) REVERT: A 90 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.6865 (tp30) REVERT: A 193 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7345 (tm-30) REVERT: A 265 GLU cc_start: 0.5553 (OUTLIER) cc_final: 0.4531 (mp0) REVERT: E 123 MET cc_start: 0.9088 (mmm) cc_final: 0.8837 (tpp) outliers start: 15 outliers final: 11 residues processed: 61 average time/residue: 0.1364 time to fit residues: 9.7862 Evaluate side-chains 63 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 49 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS 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 175 LYS Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 275 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 20 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 0.2980 chunk 17 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 0.0870 chunk 22 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2016 Z= 0.160 Angle : 0.460 5.173 2718 Z= 0.242 Chirality : 0.039 0.133 325 Planarity : 0.003 0.029 343 Dihedral : 3.709 20.545 275 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 6.39 % Allowed : 30.14 % Favored : 63.47 % 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: -0.30 (0.57), residues: 250 helix: 1.73 (0.51), residues: 118 sheet: -3.56 (0.63), residues: 39 loop : -1.13 (0.68), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 304 HIS 0.001 0.000 HIS A 272 PHE 0.009 0.001 PHE A 335 TYR 0.005 0.001 TYR A 259 ARG 0.001 0.000 ARG A 308 ********************** 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 64 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 50 time to evaluate : 0.246 Fit side-chains REVERT: A 58 ARG cc_start: 0.8386 (ttm170) cc_final: 0.8081 (mtm180) REVERT: A 74 HIS cc_start: 0.6415 (OUTLIER) cc_final: 0.5701 (t70) REVERT: A 90 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6805 (tp30) REVERT: A 193 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7335 (tm-30) REVERT: A 265 GLU cc_start: 0.5557 (OUTLIER) cc_final: 0.4536 (mp0) REVERT: E 123 MET cc_start: 0.9062 (mmm) cc_final: 0.8827 (tpp) outliers start: 14 outliers final: 9 residues processed: 60 average time/residue: 0.1222 time to fit residues: 8.6843 Evaluate side-chains 61 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 49 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS 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 160 MET Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 275 THR 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=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: 1.9990 chunk 3 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 23 optimal weight: 0.5980 chunk 10 optimal weight: 0.4980 chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.161588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.121870 restraints weight = 2469.670| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.68 r_work: 0.3298 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2344 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= 0.208 Angle : 0.481 5.181 2718 Z= 0.252 Chirality : 0.039 0.137 325 Planarity : 0.003 0.029 343 Dihedral : 3.635 21.360 274 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 5.94 % Allowed : 29.68 % 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: -0.28 (0.57), residues: 250 helix: 1.69 (0.51), residues: 118 sheet: -3.49 (0.65), residues: 39 loop : -1.05 (0.68), 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 0.010 0.001 PHE A 335 TYR 0.007 0.001 TYR A 259 ARG 0.001 0.000 ARG A 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 964.08 seconds wall clock time: 19 minutes 12.18 seconds (1152.18 seconds total)