Starting phenix.real_space_refine on Thu Dec 7 17:05:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4e_29718/12_2023/8g4e_29718_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4e_29718/12_2023/8g4e_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_29718/12_2023/8g4e_29718.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4e_29718/12_2023/8g4e_29718.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4e_29718/12_2023/8g4e_29718_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4e_29718/12_2023/8g4e_29718_updated.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 3097 Number of models: 1 Model: "" Number of chains: 2 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: 1826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1826 Unusual residues: {'CRO': 1} Classifications: {'peptide': 228, 'undetermined': 1} Link IDs: {'PTRANS': 10, 'TRANS': 216, None: 2} Not linked: pdbres="LEU B 64 " pdbres="CRO B 66 " 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: 2.29, per 1000 atoms: 0.74 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 - 3.50 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 665.8 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... running ksdssp... Secondary structure from input PDB file: 15 helices and 1 sheets defined 30.6% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 156 through 177 Processing helix chain 'A' and resid 180 through 189 Processing helix chain 'A' and resid 203 through 210 Processing helix chain 'A' and resid 213 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 236 through 243 Processing helix chain 'A' and resid 246 through 255 Processing helix chain 'A' and resid 269 through 276 Processing helix chain 'A' and resid 279 through 287 Processing helix chain 'A' and resid 302 through 308 Processing helix chain 'A' and resid 313 through 321 Processing helix chain 'B' and resid 2 through 7 Processing helix chain 'B' and resid 57 through 60 Processing helix chain 'B' and resid 69 through 71 No H-bonds generated for 'chain 'B' and resid 69 through 71' Processing helix chain 'B' and resid 79 through 81 No H-bonds generated for 'chain 'B' and resid 79 through 81' Processing helix chain 'B' and resid 83 through 86 No H-bonds generated for 'chain 'B' and resid 83 through 86' Processing sheet with id= A, first strand: chain 'B' and resid 25 through 36 removed outlier: 6.079A pdb=" N LEU B 119 " --> pdb=" O LEU B 15 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N GLU B 17 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ASN B 121 " --> pdb=" O GLU B 17 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ASP B 19 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE B 123 " --> pdb=" O ASP B 19 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N ASP B 21 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU B 125 " --> pdb=" O ASP B 21 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER B 175 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN B 164 " --> pdb=" O TYR B 151 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N TYR B 151 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N LYS B 166 " --> pdb=" O ASN B 149 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ASN B 149 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL B 219 " --> pdb=" O SER B 208 " (cutoff:3.500A) 143 hydrogen bonds defined for protein. 402 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: 0.76 Time building geometry restraints manager: 1.39 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: 100.58 - 107.25: 106 107.25 - 113.92: 1795 113.92 - 120.59: 1191 120.59 - 127.26: 1146 127.26 - 133.93: 40 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: 2604 3.32 - 3.85: 4879 3.85 - 4.37: 5852 4.37 - 4.90: 10430 Nonbonded interactions: 24471 Sorted by model distance: nonbonded pdb=" NE2 GLN B 183 " pdb=" OD1 ASN B 185 " model vdw 2.266 2.520 nonbonded pdb=" N ASP A 230 " pdb=" OD1 ASP A 230 " model vdw 2.330 2.520 nonbonded pdb=" OG1 THR A 202 " pdb=" ND1 HIS A 205 " model vdw 2.333 2.520 nonbonded pdb=" O PRO B 56 " pdb=" OG1 THR B 59 " model vdw 2.339 2.440 nonbonded pdb=" NZ LYS A 162 " pdb=" OE2 GLU A 166 " model vdw 2.378 2.520 ... (remaining 24466 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.590 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.850 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:12.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.210 ------------------------------------------------------------------------------- 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= 0.180 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: 0.42 (0.44), residues: 390 helix: 1.08 (0.45), residues: 137 sheet: 0.57 (0.50), residues: 121 loop : -0.75 (0.52), residues: 132 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 fitting. rotamer outliers: 7 poor density : 53 time to evaluate : 0.362 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 60 average time/residue: 1.3405 time to fit residues: 82.4781 Evaluate side-chains 43 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.379 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.5087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 B 77 HIS B 81 HIS ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3158 Z= 0.208 Angle : 0.516 5.198 4278 Z= 0.268 Chirality : 0.043 0.127 479 Planarity : 0.004 0.044 559 Dihedral : 5.728 70.926 422 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 8.02 % Allowed : 17.28 % 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: 0.47 (0.43), residues: 390 helix: 0.90 (0.44), residues: 139 sheet: 0.88 (0.50), residues: 117 loop : -0.76 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 275 HIS 0.004 0.001 HIS A 271 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 64 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 38 time to evaluate : 0.349 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 16 residues processed: 54 average time/residue: 1.2111 time to fit residues: 67.3229 Evaluate side-chains 52 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 36 time to evaluate : 0.334 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 12 residues processed: 4 average time/residue: 0.4576 time to fit residues: 2.4063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 0.0980 chunk 11 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3158 Z= 0.222 Angle : 0.519 5.531 4278 Z= 0.269 Chirality : 0.043 0.128 479 Planarity : 0.004 0.045 559 Dihedral : 5.582 70.390 422 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 7.72 % Allowed : 18.83 % Favored : 73.46 % 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: 0.55 (0.43), residues: 390 helix: 0.90 (0.44), residues: 139 sheet: 0.95 (0.50), residues: 117 loop : -0.64 (0.55), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 275 HIS 0.004 0.001 HIS A 205 PHE 0.011 0.002 PHE A 298 TYR 0.012 0.001 TYR B 200 ARG 0.004 0.000 ARG A 210 *********************** 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 61 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 36 time to evaluate : 0.361 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 15 residues processed: 52 average time/residue: 1.1420 time to fit residues: 61.3203 Evaluate side-chains 50 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 35 time to evaluate : 0.386 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 12 residues processed: 3 average time/residue: 0.5773 time to fit residues: 2.2994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 36 optimal weight: 0.0030 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3158 Z= 0.166 Angle : 0.483 6.247 4278 Z= 0.250 Chirality : 0.042 0.123 479 Planarity : 0.004 0.043 559 Dihedral : 5.499 71.587 422 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 8.33 % Allowed : 18.83 % Favored : 72.84 % 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: 0.76 (0.44), residues: 390 helix: 1.08 (0.44), residues: 139 sheet: 1.04 (0.50), residues: 117 loop : -0.50 (0.56), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 275 HIS 0.004 0.001 HIS A 271 PHE 0.008 0.001 PHE B 165 TYR 0.010 0.001 TYR B 200 ARG 0.002 0.000 ARG A 210 *********************** 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 61 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 34 time to evaluate : 0.367 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 17 residues processed: 54 average time/residue: 1.1316 time to fit residues: 63.0493 Evaluate side-chains 49 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 32 time to evaluate : 0.364 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 14 residues processed: 3 average time/residue: 0.7128 time to fit residues: 2.7100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 7 optimal weight: 0.0010 chunk 21 optimal weight: 0.7980 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1322 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= 0.213 Angle : 0.531 7.728 4278 Z= 0.271 Chirality : 0.043 0.130 479 Planarity : 0.004 0.045 559 Dihedral : 5.503 70.720 422 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 8.95 % Allowed : 18.52 % Favored : 72.53 % 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: 0.70 (0.44), residues: 390 helix: 0.98 (0.44), residues: 139 sheet: 1.04 (0.50), residues: 117 loop : -0.51 (0.56), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 275 HIS 0.004 0.001 HIS A 271 PHE 0.009 0.002 PHE A 298 TYR 0.012 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 65 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 36 time to evaluate : 0.379 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 21 residues processed: 57 average time/residue: 1.0820 time to fit residues: 63.6931 Evaluate side-chains 54 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 33 time to evaluate : 0.383 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 17 residues processed: 4 average time/residue: 0.8689 time to fit residues: 4.0883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 0.1980 chunk 30 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 0.3980 chunk 26 optimal weight: 6.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3158 Z= 0.157 Angle : 0.512 8.313 4278 Z= 0.264 Chirality : 0.042 0.126 479 Planarity : 0.004 0.043 559 Dihedral : 5.439 71.897 422 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 8.02 % Allowed : 20.37 % Favored : 71.60 % 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: 0.87 (0.44), residues: 390 helix: 1.12 (0.44), residues: 139 sheet: 1.13 (0.50), residues: 117 loop : -0.41 (0.56), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 275 HIS 0.003 0.001 HIS A 271 PHE 0.007 0.001 PHE B 165 TYR 0.010 0.001 TYR B 200 ARG 0.002 0.000 ARG A 210 *********************** 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 62 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 36 time to evaluate : 0.307 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 21 residues processed: 55 average time/residue: 1.2317 time to fit residues: 69.6857 Evaluate side-chains 56 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 35 time to evaluate : 0.381 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 17 residues processed: 4 average time/residue: 0.8363 time to fit residues: 3.9235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3158 Z= 0.195 Angle : 0.534 8.868 4278 Z= 0.274 Chirality : 0.043 0.130 479 Planarity : 0.004 0.044 559 Dihedral : 5.463 71.329 422 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 7.41 % Allowed : 20.99 % Favored : 71.60 % 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: 0.78 (0.44), residues: 390 helix: 0.93 (0.43), residues: 140 sheet: 1.15 (0.50), residues: 117 loop : -0.40 (0.56), residues: 133 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 0.008 0.001 PHE B 165 TYR 0.011 0.001 TYR B 200 ARG 0.002 0.000 ARG A 210 *********************** 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 61 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 37 time to evaluate : 0.318 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 20 residues processed: 57 average time/residue: 1.2097 time to fit residues: 70.9451 Evaluate side-chains 55 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 35 time to evaluate : 0.355 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 18 residues processed: 3 average time/residue: 0.6198 time to fit residues: 2.4405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 35 optimal weight: 0.0040 chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3158 Z= 0.158 Angle : 0.523 9.793 4278 Z= 0.266 Chirality : 0.042 0.131 479 Planarity : 0.004 0.043 559 Dihedral : 5.406 72.269 422 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 7.41 % Allowed : 21.30 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.44), residues: 390 helix: 1.01 (0.43), residues: 140 sheet: 1.20 (0.51), residues: 117 loop : -0.28 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 275 HIS 0.003 0.001 HIS A 271 PHE 0.007 0.001 PHE B 165 TYR 0.009 0.001 TYR B 200 ARG 0.003 0.000 ARG A 210 *********************** 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 60 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 36 time to evaluate : 0.347 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 21 residues processed: 56 average time/residue: 1.2264 time to fit residues: 70.6343 Evaluate side-chains 57 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 36 time to evaluate : 0.379 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 18 residues processed: 4 average time/residue: 0.9087 time to fit residues: 4.2337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3158 Z= 0.257 Angle : 0.581 10.332 4278 Z= 0.295 Chirality : 0.044 0.141 479 Planarity : 0.004 0.046 559 Dihedral : 5.555 69.981 422 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 6.48 % Allowed : 21.60 % Favored : 71.91 % 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 (0.43), residues: 390 helix: 0.58 (0.42), residues: 140 sheet: 1.17 (0.50), residues: 117 loop : -0.39 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 275 HIS 0.004 0.001 HIS A 205 PHE 0.009 0.002 PHE A 298 TYR 0.012 0.001 TYR B 200 ARG 0.004 0.001 ARG A 163 *********************** 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 60 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 39 time to evaluate : 0.332 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 20 residues processed: 57 average time/residue: 1.1584 time to fit residues: 67.9549 Evaluate side-chains 57 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 37 time to evaluate : 0.360 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 18 residues processed: 3 average time/residue: 0.1640 time to fit residues: 1.0501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 0.0870 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 0.0970 chunk 12 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1531 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= 0.144 Angle : 0.528 11.039 4278 Z= 0.269 Chirality : 0.042 0.146 479 Planarity : 0.004 0.043 559 Dihedral : 5.482 72.575 422 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 5.56 % Allowed : 23.15 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.44), residues: 390 helix: 0.86 (0.44), residues: 140 sheet: 1.22 (0.51), residues: 117 loop : -0.25 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 275 HIS 0.003 0.001 HIS A 271 PHE 0.006 0.001 PHE B 165 TYR 0.009 0.001 TYR B 200 ARG 0.003 0.000 ARG A 210 ********************** 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 fitting. rotamer outliers: 18 poor density : 37 time to evaluate : 0.419 Fit side-chains outliers start: 18 outliers final: 18 residues processed: 53 average time/residue: 1.2231 time to fit residues: 66.7772 Evaluate side-chains 51 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 33 time to evaluate : 0.376 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 17 residues processed: 1 average time/residue: 0.1606 time to fit residues: 0.6904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 0 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.149769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.118986 restraints weight = 3640.688| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.01 r_work: 0.3235 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1573 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= 0.212 Angle : 0.569 10.871 4278 Z= 0.290 Chirality : 0.043 0.158 479 Planarity : 0.004 0.045 559 Dihedral : 5.497 71.376 422 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 5.56 % Allowed : 23.77 % Favored : 70.68 % 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: 0.69 (0.44), residues: 390 helix: 0.63 (0.43), residues: 140 sheet: 1.22 (0.51), residues: 117 loop : -0.29 (0.56), residues: 133 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 0.008 0.001 PHE B 165 TYR 0.011 0.001 TYR B 200 ARG 0.003 0.000 ARG B 73 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1843.25 seconds wall clock time: 33 minutes 22.85 seconds (2002.85 seconds total)