Starting phenix.real_space_refine on Thu Nov 14 01:24:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4e_29718/11_2024/8g4e_29718.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4e_29718/11_2024/8g4e_29718.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4e_29718/11_2024/8g4e_29718.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4e_29718/11_2024/8g4e_29718.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4e_29718/11_2024/8g4e_29718.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4e_29718/11_2024/8g4e_29718.cif" } resolution = 2.98 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= 0.013 sd= 0.081 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 7 5.16 5 C 1957 2.51 5 N 543 2.21 5 O 590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 3097 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1271 Classifications: {'peptide': 168} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 163} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 478 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 4, 'TRANS': 59} Chain: "B" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1348 Unusual residues: {'CRO': 1} Classifications: {'peptide': 164, 'undetermined': 1} Link IDs: {'PTRANS': 6, 'TRANS': 157, None: 1} Not linked: pdbres="CRO B 66 " pdbres="VAL B 68 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'CRO:plan-3': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.71, per 1000 atoms: 0.88 Number of scatterers: 3097 At special positions: 0 Unit cell: (66.825, 77.9625, 66.825, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 7 16.00 O 590 8.00 N 543 7.00 C 1957 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 393.3 milliseconds 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 726 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 1 sheets defined 37.1% alpha, 28.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 155 through 178 Processing helix chain 'A' and resid 179 through 190 Processing helix chain 'A' and resid 202 through 210 Processing helix chain 'A' and resid 212 through 222 removed outlier: 3.665A pdb=" N ARG A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 244 Processing helix chain 'A' and resid 245 through 256 Processing helix chain 'A' and resid 268 through 277 Processing helix chain 'A' and resid 278 through 288 Processing helix chain 'A' and resid 301 through 309 Processing helix chain 'A' and resid 312 through 322 Processing helix chain 'B' and resid 2 through 8 Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 68 through 72 removed outlier: 3.651A pdb=" N PHE B 71 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER B 72 " --> pdb=" O GLN B 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 68 through 72' Processing helix chain 'B' and resid 78 through 81 Processing helix chain 'B' and resid 82 through 87 removed outlier: 3.535A pdb=" N SER B 86 " --> pdb=" O ASP B 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 11 through 22 removed outlier: 3.729A pdb=" N VAL B 219 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ASN B 149 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N LYS B 166 " --> pdb=" O ASN B 149 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N TYR B 151 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN B 164 " --> pdb=" O TYR B 151 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER B 175 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP B 21 " --> pdb=" O LEU B 125 " (cutoff:3.500A) 174 hydrogen bonds defined for protein. 489 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: 0.79 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1048 1.34 - 1.46: 444 1.46 - 1.57: 1654 1.57 - 1.69: 0 1.69 - 1.81: 12 Bond restraints: 3158 Sorted by residual: bond pdb=" C MET B 88 " pdb=" N PRO B 89 " ideal model delta sigma weight residual 1.333 1.367 -0.033 1.44e-02 4.82e+03 5.39e+00 bond pdb=" C1 CRO B 66 " pdb=" N2 CRO B 66 " ideal model delta sigma weight residual 1.289 1.328 -0.039 2.00e-02 2.50e+03 3.78e+00 bond pdb=" CZ CRO B 66 " pdb=" OH CRO B 66 " ideal model delta sigma weight residual 1.341 1.373 -0.032 2.00e-02 2.50e+03 2.63e+00 bond pdb=" CA1 CRO B 66 " pdb=" N1 CRO B 66 " ideal model delta sigma weight residual 1.448 1.475 -0.027 2.00e-02 2.50e+03 1.83e+00 bond pdb=" C3 CRO B 66 " pdb=" CA3 CRO B 66 " ideal model delta sigma weight residual 1.547 1.526 0.021 2.00e-02 2.50e+03 1.11e+00 ... (remaining 3153 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 4044 1.00 - 1.99: 181 1.99 - 2.99: 38 2.99 - 3.99: 12 3.99 - 4.99: 3 Bond angle restraints: 4278 Sorted by residual: angle pdb=" N GLY B 33 " pdb=" CA GLY B 33 " pdb=" C GLY B 33 " ideal model delta sigma weight residual 111.08 115.61 -4.53 1.62e+00 3.81e-01 7.83e+00 angle pdb=" N MET B 88 " pdb=" CA MET B 88 " pdb=" C MET B 88 " ideal model delta sigma weight residual 109.81 114.80 -4.99 2.21e+00 2.05e-01 5.09e+00 angle pdb=" C ASP B 129 " pdb=" CA ASP B 129 " pdb=" CB ASP B 129 " ideal model delta sigma weight residual 111.26 108.23 3.03 1.67e+00 3.59e-01 3.29e+00 angle pdb=" C ILE B 128 " pdb=" N ASP B 129 " pdb=" CA ASP B 129 " ideal model delta sigma weight residual 123.47 126.22 -2.75 1.53e+00 4.27e-01 3.24e+00 angle pdb=" CA GLY A 178 " pdb=" C GLY A 178 " pdb=" N TYR A 179 " ideal model delta sigma weight residual 118.50 116.80 1.70 9.90e-01 1.02e+00 2.95e+00 ... (remaining 4273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 1649 17.53 - 35.06: 162 35.06 - 52.60: 47 52.60 - 70.13: 13 70.13 - 87.66: 3 Dihedral angle restraints: 1874 sinusoidal: 746 harmonic: 1128 Sorted by residual: dihedral pdb=" CB GLU B 111 " pdb=" CG GLU B 111 " pdb=" CD GLU B 111 " pdb=" OE1 GLU B 111 " ideal model delta sinusoidal sigma weight residual 0.00 87.66 -87.66 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CA ASN B 23 " pdb=" CB ASN B 23 " pdb=" CG ASN B 23 " pdb=" OD1 ASN B 23 " ideal model delta sinusoidal sigma weight residual -90.00 -156.78 66.78 2 2.00e+01 2.50e-03 1.01e+01 dihedral pdb=" CG ARG A 176 " pdb=" CD ARG A 176 " pdb=" NE ARG A 176 " pdb=" CZ ARG A 176 " ideal model delta sinusoidal sigma weight residual 180.00 -136.68 -43.32 2 1.50e+01 4.44e-03 1.00e+01 ... (remaining 1871 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 239 0.023 - 0.046: 139 0.046 - 0.069: 56 0.069 - 0.092: 23 0.092 - 0.115: 22 Chirality restraints: 479 Sorted by residual: chirality pdb=" CB1 CRO B 66 " pdb=" CG1 CRO B 66 " pdb=" OG1 CRO B 66 " pdb=" CA1 CRO B 66 " both_signs ideal model delta sigma weight residual False -2.35 -2.47 0.12 2.00e-01 2.50e+01 3.33e-01 chirality pdb=" CA VAL B 12 " pdb=" N VAL B 12 " pdb=" C VAL B 12 " pdb=" CB VAL B 12 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.29e-01 chirality pdb=" CA ILE B 47 " pdb=" N ILE B 47 " pdb=" C ILE B 47 " pdb=" CB ILE B 47 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.23e-01 ... (remaining 476 not shown) Planarity restraints: 559 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB2 CRO B 66 " -0.008 2.00e-02 2.50e+03 3.30e-02 2.72e+01 pdb=" CG2 CRO B 66 " -0.046 2.00e-02 2.50e+03 pdb=" C1 CRO B 66 " 0.017 2.00e-02 2.50e+03 pdb=" C2 CRO B 66 " 0.026 2.00e-02 2.50e+03 pdb=" CA1 CRO B 66 " 0.012 2.00e-02 2.50e+03 pdb=" CA2 CRO B 66 " 0.014 2.00e-02 2.50e+03 pdb=" CA3 CRO B 66 " -0.069 2.00e-02 2.50e+03 pdb=" N2 CRO B 66 " 0.026 2.00e-02 2.50e+03 pdb=" N3 CRO B 66 " -0.014 2.00e-02 2.50e+03 pdb=" O2 CRO B 66 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 268 " -0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO A 269 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 269 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 269 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 235 " -0.022 5.00e-02 4.00e+02 3.29e-02 1.73e+00 pdb=" N PRO A 236 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 236 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 236 " -0.018 5.00e-02 4.00e+02 ... (remaining 556 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 706 2.79 - 3.32: 2581 3.32 - 3.85: 4854 3.85 - 4.37: 5790 4.37 - 4.90: 10416 Nonbonded interactions: 24347 Sorted by model distance: nonbonded pdb=" NE2 GLN B 183 " pdb=" OD1 ASN B 185 " model vdw 2.266 3.120 nonbonded pdb=" N ASP A 230 " pdb=" OD1 ASP A 230 " model vdw 2.330 3.120 nonbonded pdb=" OG1 THR A 202 " pdb=" ND1 HIS A 205 " model vdw 2.333 3.120 nonbonded pdb=" O PRO B 56 " pdb=" OG1 THR B 59 " model vdw 2.339 3.040 nonbonded pdb=" NZ LYS A 162 " pdb=" OE2 GLU A 166 " model vdw 2.378 3.120 ... (remaining 24342 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: 0.890 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.470 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 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 : 0.003 0.039 3158 Z= 0.187 Angle : 0.528 4.986 4278 Z= 0.293 Chirality : 0.040 0.115 479 Planarity : 0.004 0.041 559 Dihedral : 15.966 87.661 1148 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.16 % Allowed : 16.67 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.43), residues: 390 helix: 1.08 (0.45), residues: 137 sheet: 0.68 (0.51), residues: 117 loop : -0.82 (0.51), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 275 HIS 0.003 0.001 HIS A 205 PHE 0.008 0.001 PHE B 165 TYR 0.010 0.001 TYR B 200 ARG 0.001 0.000 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.353 Fit side-chains REVERT: A 293 ASN cc_start: 0.7980 (m-40) cc_final: 0.7628 (m110) REVERT: B 34 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7799 (mt-10) outliers start: 7 outliers final: 6 residues processed: 60 average time/residue: 1.3615 time to fit residues: 83.7421 Evaluate side-chains 44 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 115 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 0.0670 chunk 9 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN B 23 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3158 Z= 0.238 Angle : 0.558 6.490 4278 Z= 0.292 Chirality : 0.044 0.141 479 Planarity : 0.004 0.046 559 Dihedral : 7.087 69.853 433 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 6.79 % Allowed : 16.67 % Favored : 76.54 % 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: 0.76 (0.43), residues: 390 helix: 1.29 (0.43), residues: 142 sheet: 0.94 (0.51), residues: 116 loop : -0.69 (0.52), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 275 HIS 0.005 0.001 HIS A 205 PHE 0.011 0.002 PHE A 298 TYR 0.011 0.001 TYR B 200 ARG 0.002 0.000 ARG B 73 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 36 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 210 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.6859 (mpt-90) REVERT: A 291 ASP cc_start: 0.7861 (t0) cc_final: 0.7630 (t0) REVERT: A 301 THR cc_start: 0.8055 (OUTLIER) cc_final: 0.7825 (m) REVERT: B 34 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7738 (mt-10) REVERT: B 177 GLN cc_start: 0.7079 (OUTLIER) cc_final: 0.6534 (tt0) outliers start: 22 outliers final: 13 residues processed: 51 average time/residue: 1.2650 time to fit residues: 66.4029 Evaluate side-chains 49 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 33 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 177 GLN Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 216 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 9 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3158 Z= 0.218 Angle : 0.535 6.413 4278 Z= 0.280 Chirality : 0.043 0.134 479 Planarity : 0.004 0.045 559 Dihedral : 6.587 69.850 429 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 6.17 % Allowed : 19.14 % Favored : 74.69 % 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: 0.99 (0.43), residues: 390 helix: 1.52 (0.43), residues: 142 sheet: 1.19 (0.51), residues: 113 loop : -0.72 (0.51), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 275 HIS 0.004 0.001 HIS A 205 PHE 0.009 0.001 PHE A 298 TYR 0.011 0.001 TYR B 200 ARG 0.001 0.000 ARG B 73 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 36 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 210 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.6601 (mpt-90) REVERT: A 301 THR cc_start: 0.8034 (OUTLIER) cc_final: 0.7798 (m) REVERT: B 34 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7750 (mt-10) REVERT: B 177 GLN cc_start: 0.7101 (OUTLIER) cc_final: 0.6499 (tt0) outliers start: 20 outliers final: 11 residues processed: 48 average time/residue: 1.3092 time to fit residues: 64.6943 Evaluate side-chains 47 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 33 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 177 GLN Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 216 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3158 Z= 0.233 Angle : 0.541 6.980 4278 Z= 0.282 Chirality : 0.044 0.136 479 Planarity : 0.004 0.046 559 Dihedral : 6.437 68.510 427 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 7.41 % Allowed : 18.83 % Favored : 73.77 % 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: 1.02 (0.43), residues: 390 helix: 1.54 (0.43), residues: 142 sheet: 1.23 (0.51), residues: 113 loop : -0.72 (0.51), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 275 HIS 0.005 0.001 HIS A 205 PHE 0.010 0.002 PHE A 298 TYR 0.012 0.001 TYR B 200 ARG 0.003 0.000 ARG B 73 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 35 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 210 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.6462 (mpt-90) REVERT: A 301 THR cc_start: 0.8046 (OUTLIER) cc_final: 0.7809 (m) REVERT: A 313 ASP cc_start: 0.6771 (OUTLIER) cc_final: 0.6506 (t0) REVERT: B 34 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7759 (mt-10) outliers start: 24 outliers final: 14 residues processed: 51 average time/residue: 1.2611 time to fit residues: 66.2487 Evaluate side-chains 49 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 32 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 216 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 chunk 9 optimal weight: 0.3980 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 21 optimal weight: 0.5980 overall best weight: 0.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3158 Z= 0.165 Angle : 0.504 7.301 4278 Z= 0.264 Chirality : 0.042 0.128 479 Planarity : 0.004 0.044 559 Dihedral : 6.300 69.847 427 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 6.48 % Allowed : 19.75 % Favored : 73.77 % 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: 1.27 (0.43), residues: 390 helix: 1.85 (0.44), residues: 142 sheet: 1.29 (0.51), residues: 113 loop : -0.64 (0.52), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 275 HIS 0.004 0.001 HIS A 271 PHE 0.007 0.001 PHE B 165 TYR 0.009 0.001 TYR B 200 ARG 0.002 0.000 ARG B 73 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 34 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 166 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7248 (mt-10) REVERT: A 210 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7049 (mpt-90) REVERT: A 301 THR cc_start: 0.8028 (OUTLIER) cc_final: 0.7811 (m) REVERT: A 313 ASP cc_start: 0.6819 (OUTLIER) cc_final: 0.6490 (t0) REVERT: B 34 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7726 (mt-10) outliers start: 21 outliers final: 10 residues processed: 47 average time/residue: 1.2396 time to fit residues: 60.1236 Evaluate side-chains 47 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 33 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 203 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 0.0570 chunk 36 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3158 Z= 0.188 Angle : 0.537 8.630 4278 Z= 0.279 Chirality : 0.043 0.126 479 Planarity : 0.004 0.045 559 Dihedral : 5.940 68.820 424 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 6.48 % Allowed : 19.14 % Favored : 74.38 % 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: 1.25 (0.43), residues: 390 helix: 1.80 (0.44), residues: 142 sheet: 1.35 (0.50), residues: 113 loop : -0.70 (0.51), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 275 HIS 0.004 0.001 HIS A 205 PHE 0.008 0.001 PHE B 165 TYR 0.010 0.001 TYR B 200 ARG 0.002 0.000 ARG B 73 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 38 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 166 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7242 (mt-10) REVERT: A 210 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.6930 (mpt-90) REVERT: A 301 THR cc_start: 0.8033 (OUTLIER) cc_final: 0.7810 (m) REVERT: B 34 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7689 (mt-10) REVERT: B 177 GLN cc_start: 0.7170 (OUTLIER) cc_final: 0.6584 (tt0) outliers start: 21 outliers final: 12 residues processed: 51 average time/residue: 1.2709 time to fit residues: 66.6408 Evaluate side-chains 51 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 35 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 170 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 177 GLN Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 203 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3158 Z= 0.223 Angle : 0.561 9.032 4278 Z= 0.291 Chirality : 0.044 0.126 479 Planarity : 0.004 0.047 559 Dihedral : 5.847 68.212 423 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 6.17 % Allowed : 19.75 % Favored : 74.07 % 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: 1.20 (0.43), residues: 390 helix: 1.68 (0.43), residues: 142 sheet: 1.39 (0.50), residues: 113 loop : -0.67 (0.51), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 275 HIS 0.004 0.001 HIS A 205 PHE 0.008 0.002 PHE B 165 TYR 0.011 0.001 TYR B 200 ARG 0.003 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 36 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 210 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.6890 (mpt-90) REVERT: A 301 THR cc_start: 0.8016 (OUTLIER) cc_final: 0.7786 (m) REVERT: B 34 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7730 (mt-10) outliers start: 20 outliers final: 14 residues processed: 49 average time/residue: 1.3689 time to fit residues: 68.8425 Evaluate side-chains 50 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 34 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 170 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 203 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 28 optimal weight: 0.0770 chunk 33 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3158 Z= 0.183 Angle : 0.543 9.981 4278 Z= 0.283 Chirality : 0.043 0.141 479 Planarity : 0.004 0.045 559 Dihedral : 5.843 69.271 423 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 6.17 % Allowed : 19.14 % Favored : 74.69 % 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: 1.25 (0.43), residues: 390 helix: 1.73 (0.44), residues: 142 sheet: 1.22 (0.50), residues: 116 loop : -0.49 (0.52), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 275 HIS 0.004 0.001 HIS A 205 PHE 0.007 0.001 PHE B 165 TYR 0.009 0.001 TYR B 200 ARG 0.004 0.000 ARG B 73 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 35 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 210 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7094 (mpt-90) REVERT: A 301 THR cc_start: 0.8006 (OUTLIER) cc_final: 0.7780 (m) REVERT: B 34 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7676 (mt-10) outliers start: 20 outliers final: 13 residues processed: 47 average time/residue: 1.3742 time to fit residues: 66.3402 Evaluate side-chains 49 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 34 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 203 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 34 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3158 Z= 0.227 Angle : 0.576 10.592 4278 Z= 0.299 Chirality : 0.044 0.151 479 Planarity : 0.005 0.047 559 Dihedral : 5.886 68.614 423 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 5.56 % Allowed : 19.14 % Favored : 75.31 % 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: 1.10 (0.43), residues: 390 helix: 1.51 (0.43), residues: 142 sheet: 1.22 (0.50), residues: 116 loop : -0.53 (0.52), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 275 HIS 0.004 0.001 HIS A 205 PHE 0.008 0.002 PHE B 165 TYR 0.010 0.001 TYR B 200 ARG 0.005 0.000 ARG B 73 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 36 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 210 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7083 (mpt-90) REVERT: A 301 THR cc_start: 0.8015 (OUTLIER) cc_final: 0.7784 (m) REVERT: B 34 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7710 (mt-10) outliers start: 18 outliers final: 15 residues processed: 48 average time/residue: 1.2731 time to fit residues: 62.8440 Evaluate side-chains 52 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 35 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 170 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 216 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3158 Z= 0.229 Angle : 0.584 11.187 4278 Z= 0.302 Chirality : 0.044 0.172 479 Planarity : 0.005 0.047 559 Dihedral : 5.889 68.653 423 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 5.56 % Allowed : 20.06 % Favored : 74.38 % 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: 1.15 (0.43), residues: 390 helix: 1.47 (0.43), residues: 142 sheet: 1.46 (0.50), residues: 113 loop : -0.59 (0.51), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 275 HIS 0.004 0.001 HIS A 205 PHE 0.008 0.002 PHE B 165 TYR 0.010 0.001 TYR B 200 ARG 0.005 0.000 ARG B 73 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 37 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 210 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7081 (mpt-90) REVERT: A 301 THR cc_start: 0.8019 (OUTLIER) cc_final: 0.7768 (m) REVERT: B 34 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7713 (mt-10) outliers start: 18 outliers final: 16 residues processed: 49 average time/residue: 1.1958 time to fit residues: 60.3327 Evaluate side-chains 53 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 35 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 170 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 216 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 0 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.156890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.125842 restraints weight = 3583.342| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.03 r_work: 0.3238 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3158 Z= 0.211 Angle : 0.576 11.208 4278 Z= 0.299 Chirality : 0.044 0.178 479 Planarity : 0.005 0.046 559 Dihedral : 5.877 69.132 423 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 5.56 % Allowed : 20.37 % Favored : 74.07 % 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: 1.18 (0.43), residues: 390 helix: 1.48 (0.44), residues: 142 sheet: 1.48 (0.50), residues: 113 loop : -0.56 (0.51), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 275 HIS 0.004 0.001 HIS A 205 PHE 0.008 0.001 PHE B 165 TYR 0.010 0.001 TYR B 200 ARG 0.005 0.000 ARG B 73 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1728.62 seconds wall clock time: 31 minutes 42.73 seconds (1902.73 seconds total)