Starting phenix.real_space_refine on Thu Jul 18 17:24:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggq_40017/07_2024/8ggq_40017.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggq_40017/07_2024/8ggq_40017.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggq_40017/07_2024/8ggq_40017.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggq_40017/07_2024/8ggq_40017.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggq_40017/07_2024/8ggq_40017.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggq_40017/07_2024/8ggq_40017.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.025 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 13 5.16 5 C 1421 2.51 5 N 342 2.21 5 O 354 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-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 2130 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2115 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 82 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.48, per 1000 atoms: 1.16 Number of scatterers: 2130 At special positions: 0 Unit cell: (56.4005, 82.4315, 63.3421, 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 13 16.00 O 354 8.00 N 342 7.00 C 1421 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 492.3 milliseconds 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 538 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 0 sheets defined 87.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'R' and resid 32 through 61 removed outlier: 4.200A pdb=" N GLY R 37 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N MET R 40 " --> pdb=" O MET R 36 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 97 removed outlier: 3.881A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.562A pdb=" N SER R 137 " --> pdb=" O PHE R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 171 removed outlier: 4.030A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 178 through 187 removed outlier: 3.648A pdb=" N ILE R 182 " --> pdb=" O HIS R 178 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN R 183 " --> pdb=" O GLN R 179 " (cutoff:3.500A) Processing helix chain 'R' and resid 196 through 208 Processing helix chain 'R' and resid 208 through 236 Processing helix chain 'R' and resid 270 through 299 removed outlier: 3.936A pdb=" N THR R 274 " --> pdb=" O LYS R 270 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.658A pdb=" N VAL R 292 " --> pdb=" O PRO R 288 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 327 removed outlier: 3.597A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN R 322 " --> pdb=" O ASN R 318 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 340 166 hydrogen bonds defined for protein. 498 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: 0.51 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 637 1.34 - 1.46: 456 1.46 - 1.57: 1074 1.57 - 1.69: 1 1.69 - 1.81: 17 Bond restraints: 2185 Sorted by residual: bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.576 -0.053 2.00e-02 2.50e+03 6.99e+00 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.450 -0.053 2.00e-02 2.50e+03 6.93e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.440 -0.046 2.00e-02 2.50e+03 5.30e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.562 -0.042 2.00e-02 2.50e+03 4.47e+00 bond pdb=" CAI G1I R 501 " pdb=" NAN G1I R 501 " ideal model delta sigma weight residual 1.451 1.484 -0.033 2.00e-02 2.50e+03 2.71e+00 ... (remaining 2180 not shown) Histogram of bond angle deviations from ideal: 100.85 - 107.50: 60 107.50 - 114.14: 1288 114.14 - 120.78: 1028 120.78 - 127.42: 596 127.42 - 134.06: 24 Bond angle restraints: 2996 Sorted by residual: angle pdb=" C VAL R 87 " pdb=" CA VAL R 87 " pdb=" CB VAL R 87 " ideal model delta sigma weight residual 114.00 110.81 3.19 1.31e+00 5.83e-01 5.95e+00 angle pdb=" C VAL R 86 " pdb=" N VAL R 87 " pdb=" CA VAL R 87 " ideal model delta sigma weight residual 120.33 122.16 -1.83 8.00e-01 1.56e+00 5.23e+00 angle pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " pdb=" CAI G1I R 501 " ideal model delta sigma weight residual 110.89 117.04 -6.15 3.00e+00 1.11e-01 4.20e+00 angle pdb=" N CYS R 327 " pdb=" CA CYS R 327 " pdb=" C CYS R 327 " ideal model delta sigma weight residual 110.06 112.70 -2.64 1.43e+00 4.89e-01 3.41e+00 angle pdb=" N LYS R 149 " pdb=" CA LYS R 149 " pdb=" C LYS R 149 " ideal model delta sigma weight residual 113.50 111.33 2.17 1.23e+00 6.61e-01 3.11e+00 ... (remaining 2991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.75: 1090 13.75 - 27.49: 117 27.49 - 41.24: 34 41.24 - 54.99: 4 54.99 - 68.73: 1 Dihedral angle restraints: 1246 sinusoidal: 418 harmonic: 828 Sorted by residual: dihedral pdb=" CB CYS R 106 " pdb=" SG CYS R 106 " pdb=" SG CYS R 191 " pdb=" CB CYS R 191 " ideal model delta sinusoidal sigma weight residual -86.00 -154.73 68.73 1 1.00e+01 1.00e-02 6.12e+01 dihedral pdb=" CA PHE R 208 " pdb=" C PHE R 208 " pdb=" N TYR R 209 " pdb=" CA TYR R 209 " ideal model delta harmonic sigma weight residual 180.00 -161.20 -18.80 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA HIS R 178 " pdb=" C HIS R 178 " pdb=" N GLN R 179 " pdb=" CA GLN R 179 " ideal model delta harmonic sigma weight residual -180.00 -162.93 -17.07 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 1243 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 224 0.031 - 0.061: 107 0.061 - 0.092: 26 0.092 - 0.122: 11 0.122 - 0.153: 1 Chirality restraints: 369 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.55 -0.15 2.00e-01 2.50e+01 5.82e-01 chirality pdb=" CA TRP R 286 " pdb=" N TRP R 286 " pdb=" C TRP R 286 " pdb=" CB TRP R 286 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.62e-01 chirality pdb=" CA PRO R 168 " pdb=" N PRO R 168 " pdb=" C PRO R 168 " pdb=" CB PRO R 168 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.42e-01 ... (remaining 366 not shown) Planarity restraints: 359 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 277 " -0.007 2.00e-02 2.50e+03 1.30e-02 1.70e+00 pdb=" C ILE R 277 " 0.023 2.00e-02 2.50e+03 pdb=" O ILE R 277 " -0.008 2.00e-02 2.50e+03 pdb=" N ILE R 278 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL R 210 " 0.018 5.00e-02 4.00e+02 2.65e-02 1.12e+00 pdb=" N PRO R 211 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO R 211 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO R 211 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 322 " 0.017 5.00e-02 4.00e+02 2.50e-02 1.00e+00 pdb=" N PRO R 323 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO R 323 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO R 323 " 0.014 5.00e-02 4.00e+02 ... (remaining 356 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 651 2.83 - 3.35: 2110 3.35 - 3.87: 3364 3.87 - 4.38: 3493 4.38 - 4.90: 6394 Nonbonded interactions: 16012 Sorted by model distance: nonbonded pdb=" OG SER R 203 " pdb=" OAL G1I R 501 " model vdw 2.313 2.440 nonbonded pdb=" O ALA R 92 " pdb=" OG1 THR R 96 " model vdw 2.484 2.440 nonbonded pdb=" N ASN R 196 " pdb=" OD1 ASN R 196 " model vdw 2.522 2.520 nonbonded pdb=" OG SER R 165 " pdb=" N PHE R 166 " model vdw 2.539 2.520 nonbonded pdb=" N THR R 66 " pdb=" O THR R 66 " model vdw 2.600 2.496 ... (remaining 16007 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.050 Find NCS groups from input model: 0.020 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 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 : 0.004 0.053 2185 Z= 0.255 Angle : 0.551 6.147 2996 Z= 0.306 Chirality : 0.038 0.153 369 Planarity : 0.003 0.026 359 Dihedral : 12.049 54.423 705 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.50), residues: 277 helix: 2.36 (0.36), residues: 203 sheet: None (None), residues: 0 loop : -0.64 (0.70), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 109 HIS 0.007 0.002 HIS R 296 PHE 0.012 0.001 PHE R 282 TYR 0.009 0.001 TYR R 219 ARG 0.002 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.229 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2322 time to fit residues: 5.8769 Evaluate side-chains 18 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.8255 moved from start: 0.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2185 Z= 0.232 Angle : 0.492 5.628 2996 Z= 0.281 Chirality : 0.039 0.129 369 Planarity : 0.003 0.028 359 Dihedral : 4.459 18.432 313 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.48 % Allowed : 7.21 % Favored : 92.31 % 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: 2.61 (0.51), residues: 277 helix: 2.43 (0.35), residues: 217 sheet: None (None), residues: 0 loop : -1.01 (0.80), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.004 0.002 HIS R 296 PHE 0.013 0.001 PHE R 282 TYR 0.007 0.001 TYR R 199 ARG 0.002 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.208 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 22 average time/residue: 0.1432 time to fit residues: 3.8079 Evaluate side-chains 21 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.8284 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2185 Z= 0.245 Angle : 0.486 5.339 2996 Z= 0.278 Chirality : 0.039 0.127 369 Planarity : 0.003 0.028 359 Dihedral : 4.417 20.068 313 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 1.92 % Allowed : 12.02 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.52), residues: 277 helix: 2.60 (0.35), residues: 211 sheet: None (None), residues: 0 loop : -0.96 (0.82), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.002 0.001 HIS R 93 PHE 0.013 0.001 PHE R 282 TYR 0.007 0.001 TYR R 199 ARG 0.003 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 21 time to evaluate : 0.219 Fit side-chains REVERT: R 63 ARG cc_start: 0.3724 (mmt90) cc_final: 0.1881 (ttm170) REVERT: R 72 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8269 (mp) outliers start: 4 outliers final: 2 residues processed: 24 average time/residue: 0.1588 time to fit residues: 4.5971 Evaluate side-chains 24 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 21 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 0.0970 chunk 23 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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: 0.8258 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2185 Z= 0.200 Angle : 0.449 4.933 2996 Z= 0.256 Chirality : 0.038 0.122 369 Planarity : 0.003 0.027 359 Dihedral : 4.242 18.857 313 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.44 % Allowed : 14.90 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.52), residues: 277 helix: 2.40 (0.35), residues: 223 sheet: None (None), residues: 0 loop : -0.68 (0.91), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.002 0.001 HIS R 296 PHE 0.012 0.001 PHE R 282 TYR 0.006 0.001 TYR R 199 ARG 0.002 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 0.205 Fit side-chains REVERT: R 63 ARG cc_start: 0.3731 (mmt90) cc_final: 0.1901 (ttm170) outliers start: 3 outliers final: 2 residues processed: 22 average time/residue: 0.1676 time to fit residues: 4.4192 Evaluate side-chains 22 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 20 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 6 optimal weight: 0.0020 chunk 27 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- 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: 0.8251 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2185 Z= 0.191 Angle : 0.438 4.916 2996 Z= 0.250 Chirality : 0.038 0.121 369 Planarity : 0.003 0.026 359 Dihedral : 4.150 18.927 313 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 2.40 % Allowed : 14.90 % Favored : 82.69 % 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: 2.89 (0.52), residues: 277 helix: 2.51 (0.35), residues: 223 sheet: None (None), residues: 0 loop : -0.74 (0.90), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.002 0.001 HIS R 178 PHE 0.012 0.001 PHE R 282 TYR 0.006 0.001 TYR R 199 ARG 0.001 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 23 time to evaluate : 0.222 Fit side-chains REVERT: R 63 ARG cc_start: 0.3750 (mmt90) cc_final: 0.1903 (ttm170) REVERT: R 72 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8302 (mt) outliers start: 5 outliers final: 3 residues processed: 27 average time/residue: 0.1267 time to fit residues: 4.1560 Evaluate side-chains 25 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 21 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 0.9990 chunk 3 optimal weight: 0.0370 chunk 15 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 10 optimal weight: 0.3980 chunk 8 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.4858 ------------------------------------------------------------------------------- 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: 0.8235 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2185 Z= 0.177 Angle : 0.428 4.905 2996 Z= 0.245 Chirality : 0.037 0.120 369 Planarity : 0.003 0.026 359 Dihedral : 4.070 18.884 313 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.92 % Allowed : 17.79 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.52), residues: 277 helix: 2.51 (0.35), residues: 224 sheet: None (None), residues: 0 loop : -0.70 (0.92), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.003 0.001 HIS R 178 PHE 0.011 0.001 PHE R 282 TYR 0.006 0.001 TYR R 199 ARG 0.002 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 22 time to evaluate : 0.227 Fit side-chains REVERT: R 63 ARG cc_start: 0.3797 (mmt90) cc_final: 0.1959 (ttm170) REVERT: R 72 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8304 (mt) outliers start: 4 outliers final: 3 residues processed: 26 average time/residue: 0.1521 time to fit residues: 4.7878 Evaluate side-chains 25 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 21 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 24 optimal weight: 0.0000 chunk 25 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 7 optimal weight: 0.0770 overall best weight: 0.3942 ------------------------------------------------------------------------------- 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: 0.8210 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 2185 Z= 0.158 Angle : 0.413 4.894 2996 Z= 0.235 Chirality : 0.037 0.118 369 Planarity : 0.003 0.025 359 Dihedral : 3.955 18.895 313 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.92 % Allowed : 18.75 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.07 (0.52), residues: 277 helix: 2.62 (0.35), residues: 224 sheet: None (None), residues: 0 loop : -0.69 (0.92), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.001 0.001 HIS R 296 PHE 0.011 0.001 PHE R 282 TYR 0.006 0.001 TYR R 308 ARG 0.001 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 21 time to evaluate : 0.223 Fit side-chains REVERT: R 63 ARG cc_start: 0.3781 (mmt90) cc_final: 0.1989 (ttm170) REVERT: R 72 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8278 (mt) outliers start: 4 outliers final: 3 residues processed: 25 average time/residue: 0.1540 time to fit residues: 4.6703 Evaluate side-chains 25 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 21 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 26 optimal weight: 0.0980 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.2980 chunk 27 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 13 optimal weight: 3.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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: 0.8206 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 2185 Z= 0.158 Angle : 0.409 4.901 2996 Z= 0.233 Chirality : 0.037 0.116 369 Planarity : 0.003 0.024 359 Dihedral : 3.887 18.703 313 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.92 % Allowed : 18.27 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.15 (0.52), residues: 277 helix: 2.69 (0.35), residues: 224 sheet: None (None), residues: 0 loop : -0.68 (0.93), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.002 0.001 HIS R 296 PHE 0.011 0.001 PHE R 282 TYR 0.006 0.001 TYR R 199 ARG 0.001 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 22 time to evaluate : 0.218 Fit side-chains REVERT: R 63 ARG cc_start: 0.3778 (mmt90) cc_final: 0.1988 (ttm170) REVERT: R 72 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8277 (mt) outliers start: 4 outliers final: 3 residues processed: 26 average time/residue: 0.1424 time to fit residues: 4.5091 Evaluate side-chains 25 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 21 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 0.9990 chunk 23 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.8259 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2185 Z= 0.216 Angle : 0.447 4.971 2996 Z= 0.256 Chirality : 0.038 0.117 369 Planarity : 0.003 0.025 359 Dihedral : 4.029 18.648 313 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.40 % Allowed : 18.75 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.52), residues: 277 helix: 2.53 (0.35), residues: 225 sheet: None (None), residues: 0 loop : -1.09 (0.88), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.003 0.001 HIS R 296 PHE 0.013 0.001 PHE R 282 TYR 0.008 0.001 TYR R 199 ARG 0.002 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 22 time to evaluate : 0.219 Fit side-chains REVERT: R 63 ARG cc_start: 0.3848 (mmt90) cc_final: 0.2091 (ttm170) REVERT: R 72 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8302 (mt) REVERT: R 115 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7896 (tp) outliers start: 5 outliers final: 3 residues processed: 27 average time/residue: 0.1485 time to fit residues: 4.8563 Evaluate side-chains 27 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 22 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 16 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 0.0040 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 overall best weight: 0.4992 ------------------------------------------------------------------------------- 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: 0.8237 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2185 Z= 0.182 Angle : 0.426 4.930 2996 Z= 0.244 Chirality : 0.037 0.118 369 Planarity : 0.003 0.025 359 Dihedral : 4.004 18.825 313 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.92 % Allowed : 19.23 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.93 (0.52), residues: 277 helix: 2.59 (0.35), residues: 225 sheet: None (None), residues: 0 loop : -1.15 (0.85), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.002 0.001 HIS R 296 PHE 0.011 0.001 PHE R 282 TYR 0.006 0.001 TYR R 199 ARG 0.002 0.000 ARG R 239 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 23 time to evaluate : 0.219 Fit side-chains REVERT: R 63 ARG cc_start: 0.3827 (mmt90) cc_final: 0.2013 (ttm170) REVERT: R 72 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8293 (mt) outliers start: 4 outliers final: 3 residues processed: 26 average time/residue: 0.1531 time to fit residues: 4.7908 Evaluate side-chains 27 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 23 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 26 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 11 optimal weight: 0.0570 chunk 2 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 0.1980 chunk 9 optimal weight: 0.5980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.135242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.120540 restraints weight = 2911.023| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.58 r_work: 0.3220 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3107 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3107 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2185 Z= 0.168 Angle : 0.418 4.907 2996 Z= 0.238 Chirality : 0.037 0.117 369 Planarity : 0.003 0.024 359 Dihedral : 3.945 18.839 313 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.88 % Allowed : 17.79 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.96 (0.52), residues: 277 helix: 2.63 (0.35), residues: 225 sheet: None (None), residues: 0 loop : -1.22 (0.85), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.002 0.001 HIS R 296 PHE 0.011 0.001 PHE R 282 TYR 0.006 0.001 TYR R 199 ARG 0.001 0.000 ARG R 239 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 946.48 seconds wall clock time: 19 minutes 58.10 seconds (1198.10 seconds total)