Starting phenix.real_space_refine on Fri Apr 5 12:23:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggp_40016/04_2024/8ggp_40016_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggp_40016/04_2024/8ggp_40016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggp_40016/04_2024/8ggp_40016.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggp_40016/04_2024/8ggp_40016.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggp_40016/04_2024/8ggp_40016_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggp_40016/04_2024/8ggp_40016_updated.pdb" } resolution = 3.2 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= 0.027 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 1394 2.51 5 N 328 2.21 5 O 340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 2075 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2060 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 7, 'TRANS': 272} Chain breaks: 1 Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 239 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 6, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 115 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: 1.83, per 1000 atoms: 0.88 Number of scatterers: 2075 At special positions: 0 Unit cell: (57.2682, 80.6961, 62.4744, 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 340 8.00 N 328 7.00 C 1394 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: 0.85 Conformation dependent library (CDL) restraints added in 420.1 milliseconds 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 538 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 13 helices and 0 sheets defined 81.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'R' and resid 33 through 60 removed outlier: 3.578A pdb=" N GLY R 37 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 64 No H-bonds generated for 'chain 'R' and resid 62 through 64' Processing helix chain 'R' and resid 67 through 96 removed outlier: 4.135A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL R 86 " --> pdb=" O MET R 82 " (cutoff:3.500A) removed outlier: 5.176A 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 103 through 136 removed outlier: 3.501A pdb=" N SER R 120 " --> pdb=" O CYS R 116 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS R 125 " --> pdb=" O ILE R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 141 through 144 No H-bonds generated for 'chain 'R' and resid 141 through 144' Processing helix chain 'R' and resid 147 through 170 removed outlier: 3.778A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 4.091A 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 179 through 186 Processing helix chain 'R' and resid 197 through 207 removed outlier: 3.718A pdb=" N VAL R 206 " --> pdb=" O ALA R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 236 Processing helix chain 'R' and resid 272 through 298 removed outlier: 4.093A pdb=" N THR R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.508A pdb=" N VAL R 292 " --> pdb=" O PRO R 288 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 319 removed outlier: 3.821A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) Processing helix chain 'R' and resid 322 through 326 Processing helix chain 'R' and resid 330 through 339 144 hydrogen bonds defined for protein. 432 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: 0.41 Time building geometry restraints manager: 0.93 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: 615 1.34 - 1.46: 495 1.46 - 1.58: 1004 1.58 - 1.70: 0 1.70 - 1.82: 17 Bond restraints: 2131 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.448 -0.051 2.00e-02 2.50e+03 6.50e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.442 -0.048 2.00e-02 2.50e+03 5.73e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.569 -0.046 2.00e-02 2.50e+03 5.25e+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=" CAE G1I R 501 " pdb=" CAG G1I R 501 " ideal model delta sigma weight residual 1.506 1.537 -0.031 2.00e-02 2.50e+03 2.44e+00 ... (remaining 2126 not shown) Histogram of bond angle deviations from ideal: 100.68 - 107.33: 56 107.33 - 113.99: 1249 113.99 - 120.64: 924 120.64 - 127.29: 678 127.29 - 133.95: 26 Bond angle restraints: 2933 Sorted by residual: angle pdb=" C SER R 207 " pdb=" N PHE R 208 " pdb=" CA PHE R 208 " ideal model delta sigma weight residual 122.46 119.21 3.25 1.80e+00 3.09e-01 3.26e+00 angle pdb=" CAE G1I R 501 " pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 112.63 118.04 -5.41 3.00e+00 1.11e-01 3.25e+00 angle pdb=" N VAL R 87 " pdb=" CA VAL R 87 " pdb=" C VAL R 87 " ideal model delta sigma weight residual 108.88 112.53 -3.65 2.16e+00 2.14e-01 2.86e+00 angle pdb=" C THR R 96 " pdb=" N LYS R 97 " pdb=" CA LYS R 97 " ideal model delta sigma weight residual 124.31 127.13 -2.82 1.67e+00 3.59e-01 2.85e+00 angle pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " pdb=" CAI G1I R 501 " ideal model delta sigma weight residual 110.89 115.86 -4.97 3.00e+00 1.11e-01 2.75e+00 ... (remaining 2928 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.65: 1053 12.65 - 25.30: 111 25.30 - 37.95: 28 37.95 - 50.60: 12 50.60 - 63.25: 1 Dihedral angle restraints: 1205 sinusoidal: 378 harmonic: 827 Sorted by residual: 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 -162.43 -17.57 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA VAL R 295 " pdb=" C VAL R 295 " pdb=" N HIS R 296 " pdb=" CA HIS R 296 " ideal model delta harmonic sigma weight residual 180.00 -164.96 -15.04 0 5.00e+00 4.00e-02 9.04e+00 dihedral pdb=" CA ARG R 151 " pdb=" CB ARG R 151 " pdb=" CG ARG R 151 " pdb=" CD ARG R 151 " ideal model delta sinusoidal sigma weight residual -180.00 -130.02 -49.98 3 1.50e+01 4.44e-03 8.84e+00 ... (remaining 1202 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 226 0.030 - 0.059: 101 0.059 - 0.089: 25 0.089 - 0.119: 14 0.119 - 0.149: 1 Chirality restraints: 367 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 5.51e-01 chirality pdb=" CA TRP R 313 " pdb=" N TRP R 313 " pdb=" C TRP R 313 " pdb=" CB TRP R 313 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.42e-01 chirality pdb=" CA PRO R 138 " pdb=" N PRO R 138 " pdb=" C PRO R 138 " pdb=" CB PRO R 138 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.05e-01 ... (remaining 364 not shown) Planarity restraints: 351 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 313 " -0.007 2.00e-02 2.50e+03 9.51e-03 2.26e+00 pdb=" CG TRP R 313 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP R 313 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP R 313 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP R 313 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP R 313 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 313 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 313 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 313 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP R 313 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN R 322 " 0.016 5.00e-02 4.00e+02 2.37e-02 8.98e-01 pdb=" N PRO R 323 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO R 323 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO R 323 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL R 210 " 0.014 5.00e-02 4.00e+02 2.10e-02 7.03e-01 pdb=" N PRO R 211 " -0.036 5.00e-02 4.00e+02 pdb=" CA PRO R 211 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO R 211 " 0.012 5.00e-02 4.00e+02 ... (remaining 348 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 591 2.82 - 3.34: 2055 3.34 - 3.86: 3330 3.86 - 4.38: 3435 4.38 - 4.90: 6324 Nonbonded interactions: 15735 Sorted by model distance: nonbonded pdb=" OG SER R 203 " pdb=" OAL G1I R 501 " model vdw 2.298 2.440 nonbonded pdb=" O LEU R 64 " pdb=" ND2 ASN R 69 " model vdw 2.305 2.520 nonbonded pdb=" O SER R 137 " pdb=" OG SER R 137 " model vdw 2.344 2.440 nonbonded pdb=" O THR R 189 " pdb=" OG1 THR R 189 " model vdw 2.491 2.440 nonbonded pdb=" OD1 ASN R 196 " pdb=" N GLN R 197 " model vdw 2.513 2.520 ... (remaining 15730 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 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: 7.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.200 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 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 0.051 2131 Z= 0.249 Angle : 0.520 5.412 2933 Z= 0.285 Chirality : 0.039 0.149 367 Planarity : 0.003 0.024 351 Dihedral : 12.492 63.247 664 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.51), residues: 276 helix: 1.93 (0.35), residues: 220 sheet: None (None), residues: 0 loop : -1.52 (0.69), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 313 HIS 0.003 0.001 HIS R 93 PHE 0.010 0.001 PHE R 217 TYR 0.010 0.001 TYR R 174 ARG 0.001 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.199 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1186 time to fit residues: 2.8910 Evaluate side-chains 17 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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: 0.7980 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 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: 0.8121 moved from start: 0.0585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2131 Z= 0.244 Angle : 0.479 5.455 2933 Z= 0.268 Chirality : 0.039 0.129 367 Planarity : 0.003 0.022 351 Dihedral : 4.385 17.344 309 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.03 % Allowed : 5.15 % Favored : 93.81 % 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: 1.91 (0.51), residues: 276 helix: 1.95 (0.35), residues: 224 sheet: None (None), residues: 0 loop : -1.85 (0.69), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 313 HIS 0.004 0.001 HIS R 296 PHE 0.010 0.001 PHE R 217 TYR 0.008 0.001 TYR R 174 ARG 0.001 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 14 time to evaluate : 0.226 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 16 average time/residue: 0.1152 time to fit residues: 2.4903 Evaluate side-chains 16 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 14 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 13 optimal weight: 0.0070 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 24 optimal weight: 0.2980 overall best weight: 0.4398 ------------------------------------------------------------------------------- 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: 0.8067 moved from start: 0.0700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2131 Z= 0.164 Angle : 0.435 5.389 2933 Z= 0.240 Chirality : 0.038 0.123 367 Planarity : 0.003 0.022 351 Dihedral : 4.165 17.535 309 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.55 % Allowed : 8.76 % Favored : 89.69 % 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: 2.17 (0.51), residues: 276 helix: 2.12 (0.35), residues: 225 sheet: None (None), residues: 0 loop : -1.80 (0.73), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 313 HIS 0.002 0.001 HIS R 93 PHE 0.008 0.001 PHE R 217 TYR 0.006 0.001 TYR R 308 ARG 0.001 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 15 time to evaluate : 0.222 Fit side-chains REVERT: R 40 MET cc_start: 0.7321 (mtt) cc_final: 0.7074 (mtt) outliers start: 3 outliers final: 2 residues processed: 18 average time/residue: 0.1170 time to fit residues: 2.7941 Evaluate side-chains 16 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 14 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8120 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2131 Z= 0.232 Angle : 0.466 5.453 2933 Z= 0.259 Chirality : 0.039 0.127 367 Planarity : 0.003 0.024 351 Dihedral : 4.297 17.363 309 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.03 % Allowed : 12.89 % Favored : 86.08 % 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: 2.05 (0.51), residues: 276 helix: 2.04 (0.35), residues: 225 sheet: None (None), residues: 0 loop : -1.87 (0.74), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 313 HIS 0.003 0.001 HIS R 296 PHE 0.009 0.001 PHE R 290 TYR 0.007 0.001 TYR R 199 ARG 0.001 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 14 time to evaluate : 0.195 Fit side-chains REVERT: R 40 MET cc_start: 0.7410 (mtt) cc_final: 0.7141 (mtt) outliers start: 2 outliers final: 2 residues processed: 16 average time/residue: 0.1116 time to fit residues: 2.4099 Evaluate side-chains 16 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 14 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 9 optimal weight: 0.7980 chunk 24 optimal weight: 0.3980 chunk 5 optimal weight: 0.9980 chunk 15 optimal weight: 0.0870 chunk 6 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 22 optimal weight: 0.3980 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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: 0.8076 moved from start: 0.0862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2131 Z= 0.167 Angle : 0.430 5.408 2933 Z= 0.237 Chirality : 0.038 0.124 367 Planarity : 0.003 0.024 351 Dihedral : 4.144 17.628 309 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.55 % Allowed : 12.37 % Favored : 86.08 % 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: 2.25 (0.51), residues: 276 helix: 2.19 (0.35), residues: 225 sheet: None (None), residues: 0 loop : -1.82 (0.76), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 313 HIS 0.002 0.001 HIS R 93 PHE 0.009 0.001 PHE R 217 TYR 0.006 0.001 TYR R 308 ARG 0.002 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 14 time to evaluate : 0.222 Fit side-chains REVERT: R 40 MET cc_start: 0.7284 (mtt) cc_final: 0.7039 (mtt) outliers start: 3 outliers final: 2 residues processed: 17 average time/residue: 0.1114 time to fit residues: 2.5417 Evaluate side-chains 16 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 14 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 0.4980 chunk 3 optimal weight: 0.0770 chunk 15 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 0.1980 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 17 optimal weight: 0.3980 overall best weight: 0.3538 ------------------------------------------------------------------------------- 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: 0.8035 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2131 Z= 0.142 Angle : 0.414 5.391 2933 Z= 0.226 Chirality : 0.037 0.118 367 Planarity : 0.003 0.023 351 Dihedral : 3.990 17.388 309 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.55 % Allowed : 13.92 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.51), residues: 276 helix: 2.34 (0.35), residues: 225 sheet: None (None), residues: 0 loop : -1.78 (0.77), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 313 HIS 0.002 0.001 HIS R 93 PHE 0.007 0.001 PHE R 282 TYR 0.006 0.001 TYR R 308 ARG 0.002 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 16 time to evaluate : 0.224 Fit side-chains REVERT: R 40 MET cc_start: 0.7205 (mtt) cc_final: 0.6959 (mtt) outliers start: 3 outliers final: 2 residues processed: 19 average time/residue: 0.1011 time to fit residues: 2.5805 Evaluate side-chains 16 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 14 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 0.5980 chunk 13 optimal weight: 0.0070 chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 0.0370 chunk 19 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 overall best weight: 0.3876 ------------------------------------------------------------------------------- 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: 0.8044 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 : 0.002 0.017 2131 Z= 0.149 Angle : 0.416 5.402 2933 Z= 0.228 Chirality : 0.037 0.120 367 Planarity : 0.003 0.023 351 Dihedral : 3.981 17.170 309 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.55 % Allowed : 14.43 % Favored : 84.02 % 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: 2.48 (0.51), residues: 276 helix: 2.35 (0.35), residues: 225 sheet: None (None), residues: 0 loop : -1.78 (0.77), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.002 0.001 HIS R 93 PHE 0.007 0.001 PHE R 217 TYR 0.006 0.001 TYR R 308 ARG 0.001 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 15 time to evaluate : 0.223 Fit side-chains REVERT: R 40 MET cc_start: 0.7273 (mtt) cc_final: 0.7016 (mtt) outliers start: 3 outliers final: 2 residues processed: 18 average time/residue: 0.1075 time to fit residues: 2.6059 Evaluate side-chains 17 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 15 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 0.0060 chunk 2 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 overall best weight: 0.6596 ------------------------------------------------------------------------------- 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: 0.8093 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2131 Z= 0.211 Angle : 0.442 5.460 2933 Z= 0.246 Chirality : 0.038 0.124 367 Planarity : 0.003 0.024 351 Dihedral : 4.151 16.965 309 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.55 % Allowed : 14.43 % Favored : 84.02 % 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: 2.22 (0.51), residues: 276 helix: 2.19 (0.35), residues: 225 sheet: None (None), residues: 0 loop : -1.97 (0.74), residues: 51 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 0.008 0.001 PHE R 282 TYR 0.007 0.001 TYR R 132 ARG 0.001 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 15 time to evaluate : 0.189 Fit side-chains REVERT: R 40 MET cc_start: 0.7397 (mtt) cc_final: 0.7132 (mtt) outliers start: 3 outliers final: 3 residues processed: 17 average time/residue: 0.1020 time to fit residues: 2.3455 Evaluate side-chains 18 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 15 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 0.6980 chunk 23 optimal weight: 0.0060 chunk 6 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 3 optimal weight: 0.0870 chunk 22 optimal weight: 0.1980 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: 0.3174 ------------------------------------------------------------------------------- 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: 0.8031 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2131 Z= 0.133 Angle : 0.409 5.393 2933 Z= 0.223 Chirality : 0.037 0.118 367 Planarity : 0.003 0.023 351 Dihedral : 3.955 17.335 309 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.03 % Allowed : 14.95 % Favored : 84.02 % 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: 2.42 (0.51), residues: 276 helix: 2.33 (0.35), residues: 225 sheet: None (None), residues: 0 loop : -1.88 (0.75), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 313 HIS 0.002 0.001 HIS R 93 PHE 0.007 0.001 PHE R 217 TYR 0.006 0.001 TYR R 308 ARG 0.001 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 15 time to evaluate : 0.222 Fit side-chains REVERT: R 40 MET cc_start: 0.7197 (mtt) cc_final: 0.6939 (mtt) outliers start: 2 outliers final: 2 residues processed: 17 average time/residue: 0.1115 time to fit residues: 2.5428 Evaluate side-chains 16 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 14 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 317 VAL 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: 0.8980 chunk 14 optimal weight: 0.0050 chunk 19 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 chunk 1 optimal weight: 0.5980 chunk 26 optimal weight: 0.3980 chunk 5 optimal weight: 0.5980 overall best weight: 0.4194 ------------------------------------------------------------------------------- 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: 0.8045 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2131 Z= 0.156 Angle : 0.417 5.424 2933 Z= 0.229 Chirality : 0.037 0.118 367 Planarity : 0.003 0.023 351 Dihedral : 3.978 17.052 309 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.03 % Allowed : 14.95 % Favored : 84.02 % 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: 2.37 (0.51), residues: 276 helix: 2.29 (0.35), residues: 225 sheet: None (None), residues: 0 loop : -1.91 (0.74), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.002 0.001 HIS R 93 PHE 0.007 0.001 PHE R 282 TYR 0.006 0.001 TYR R 308 ARG 0.001 0.000 ARG R 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 14 time to evaluate : 0.225 Fit side-chains REVERT: R 40 MET cc_start: 0.7285 (mtt) cc_final: 0.7025 (mtt) outliers start: 2 outliers final: 2 residues processed: 16 average time/residue: 0.1066 time to fit residues: 2.2718 Evaluate side-chains 16 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 14 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 3 optimal weight: 0.0050 chunk 5 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 26 optimal weight: 0.1980 chunk 0 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 178 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.135986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.119209 restraints weight = 2852.219| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.87 r_work: 0.3269 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2131 Z= 0.185 Angle : 0.432 5.454 2933 Z= 0.239 Chirality : 0.038 0.120 367 Planarity : 0.003 0.024 351 Dihedral : 4.077 16.941 309 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.03 % Allowed : 14.95 % Favored : 84.02 % 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: 2.25 (0.51), residues: 276 helix: 2.21 (0.35), residues: 225 sheet: None (None), residues: 0 loop : -1.96 (0.74), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.003 0.001 HIS R 296 PHE 0.008 0.001 PHE R 290 TYR 0.006 0.001 TYR R 132 ARG 0.001 0.000 ARG R 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 947.27 seconds wall clock time: 17 minutes 27.00 seconds (1047.00 seconds total)