Starting phenix.real_space_refine on Fri Apr 5 12:34:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggn_40014/04_2024/8ggn_40014_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggn_40014/04_2024/8ggn_40014.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggn_40014/04_2024/8ggn_40014.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggn_40014/04_2024/8ggn_40014.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggn_40014/04_2024/8ggn_40014_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggn_40014/04_2024/8ggn_40014_updated.pdb" } resolution = 3.3 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= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 1446 2.51 5 N 344 2.21 5 O 363 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 62": "OE1" <-> "OE2" Residue "R GLU 237": "OE1" <-> "OE2" 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: 2168 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2153 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 7, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 89 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: 1.72, per 1000 atoms: 0.79 Number of scatterers: 2168 At special positions: 0 Unit cell: (58.1359, 83.2992, 61.6067, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 363 8.00 N 344 7.00 C 1446 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: 1.11 Conformation dependent library (CDL) restraints added in 429.3 milliseconds 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 546 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 11 helices and 0 sheets defined 80.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'R' and resid 31 through 60 removed outlier: 3.753A pdb=" N MET R 36 " --> pdb=" O TRP R 32 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLY R 37 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 96 removed outlier: 4.251A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.958A 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: 3.602A pdb=" N GLU R 107 " --> pdb=" O ASN R 103 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE R 135 " --> pdb=" O ARG R 131 " (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: 3.696A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.667A 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 Processing helix chain 'R' and resid 209 through 236 Processing helix chain 'R' and resid 270 through 298 removed outlier: 4.007A pdb=" N THR R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.619A pdb=" N VAL R 292 " --> pdb=" O PRO R 288 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 326 removed outlier: 3.567A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) removed outlier: 3.670A 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 330 through 339 151 hydrogen bonds defined for protein. 453 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: 0.54 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 325 1.32 - 1.44: 650 1.44 - 1.56: 1228 1.56 - 1.69: 1 1.69 - 1.81: 21 Bond restraints: 2225 Sorted by residual: bond pdb=" CA ARG R 63 " pdb=" C ARG R 63 " ideal model delta sigma weight residual 1.522 1.479 0.043 1.37e-02 5.33e+03 9.74e+00 bond pdb=" C LEU R 64 " pdb=" O LEU R 64 " ideal model delta sigma weight residual 1.235 1.199 0.037 1.33e-02 5.65e+03 7.54e+00 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.447 -0.050 2.00e-02 2.50e+03 6.29e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.570 -0.047 2.00e-02 2.50e+03 5.56e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.441 -0.047 2.00e-02 2.50e+03 5.42e+00 ... (remaining 2220 not shown) Histogram of bond angle deviations from ideal: 100.39 - 107.11: 48 107.11 - 113.83: 1296 113.83 - 120.55: 950 120.55 - 127.26: 730 127.26 - 133.98: 26 Bond angle restraints: 3050 Sorted by residual: angle pdb=" N GLU R 62 " pdb=" CA GLU R 62 " pdb=" CB GLU R 62 " ideal model delta sigma weight residual 110.49 105.04 5.45 1.48e+00 4.57e-01 1.36e+01 angle pdb=" N GLU R 62 " pdb=" CA GLU R 62 " pdb=" C GLU R 62 " ideal model delta sigma weight residual 113.17 116.58 -3.41 1.26e+00 6.30e-01 7.33e+00 angle pdb=" N ARG R 63 " pdb=" CA ARG R 63 " pdb=" C ARG R 63 " ideal model delta sigma weight residual 113.23 109.94 3.29 1.24e+00 6.50e-01 7.02e+00 angle pdb=" C ALA R 85 " pdb=" N VAL R 86 " pdb=" CA VAL R 86 " ideal model delta sigma weight residual 120.82 117.78 3.04 1.55e+00 4.16e-01 3.85e+00 angle pdb=" CAE G1I R 501 " pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 112.63 117.96 -5.33 3.00e+00 1.11e-01 3.16e+00 ... (remaining 3045 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 1147 16.05 - 32.09: 99 32.09 - 48.14: 20 48.14 - 64.18: 2 64.18 - 80.23: 4 Dihedral angle restraints: 1272 sinusoidal: 432 harmonic: 840 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 -160.00 -20.00 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CG ARG R 175 " pdb=" CD ARG R 175 " pdb=" NE ARG R 175 " pdb=" CZ ARG R 175 " ideal model delta sinusoidal sigma weight residual -180.00 -139.14 -40.86 2 1.50e+01 4.44e-03 9.13e+00 dihedral pdb=" CB GLU R 122 " pdb=" CG GLU R 122 " pdb=" CD GLU R 122 " pdb=" OE1 GLU R 122 " ideal model delta sinusoidal sigma weight residual 0.00 80.23 -80.23 1 3.00e+01 1.11e-03 8.86e+00 ... (remaining 1269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 243 0.034 - 0.068: 99 0.068 - 0.101: 23 0.101 - 0.135: 7 0.135 - 0.169: 2 Chirality restraints: 374 Sorted by residual: chirality pdb=" CA LEU R 64 " pdb=" N LEU R 64 " pdb=" C LEU R 64 " pdb=" CB LEU R 64 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.11e-01 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 2.54 -0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CA PRO R 288 " pdb=" N PRO R 288 " pdb=" C PRO R 288 " pdb=" CB PRO R 288 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.83e-01 ... (remaining 371 not shown) Planarity restraints: 366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE R 61 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.84e+00 pdb=" C PHE R 61 " 0.042 2.00e-02 2.50e+03 pdb=" O PHE R 61 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU R 62 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 173 " -0.009 2.00e-02 2.50e+03 6.35e-03 1.01e+00 pdb=" CG TRP R 173 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP R 173 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP R 173 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 173 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP R 173 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 173 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 173 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 173 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP R 173 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL R 210 " 0.017 5.00e-02 4.00e+02 2.49e-02 9.89e-01 pdb=" N PRO R 211 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO R 211 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO R 211 " 0.014 5.00e-02 4.00e+02 ... (remaining 363 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 472 2.78 - 3.31: 2114 3.31 - 3.84: 3508 3.84 - 4.37: 3639 4.37 - 4.90: 6814 Nonbonded interactions: 16547 Sorted by model distance: nonbonded pdb=" OD2 ASP R 113 " pdb=" OAM G1I R 501 " model vdw 2.248 2.440 nonbonded pdb=" OG SER R 203 " pdb=" OAL G1I R 501 " model vdw 2.294 2.440 nonbonded pdb=" OG SER R 203 " pdb=" OAK G1I R 501 " model vdw 2.438 2.440 nonbonded pdb=" O ALA R 92 " pdb=" OG1 THR R 96 " model vdw 2.448 2.440 nonbonded pdb=" O THR R 189 " pdb=" OG1 THR R 189 " model vdw 2.462 2.440 ... (remaining 16542 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: 1.690 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: 7.220 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.840 Find NCS groups from input model: 0.060 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 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 : 0.005 0.050 2225 Z= 0.301 Angle : 0.584 5.623 3050 Z= 0.331 Chirality : 0.040 0.169 374 Planarity : 0.003 0.025 366 Dihedral : 13.181 80.230 723 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.49), residues: 281 helix: 2.30 (0.35), residues: 216 sheet: None (None), residues: 0 loop : -1.40 (0.63), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 173 HIS 0.004 0.001 HIS R 296 PHE 0.013 0.001 PHE R 108 TYR 0.010 0.001 TYR R 199 ARG 0.002 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.363 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1695 time to fit residues: 4.8869 Evaluate side-chains 18 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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: 0.6980 chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 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: 0.8285 moved from start: 0.0693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2225 Z= 0.217 Angle : 0.475 5.506 3050 Z= 0.267 Chirality : 0.038 0.126 374 Planarity : 0.003 0.027 366 Dihedral : 4.759 20.231 316 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.93 % Allowed : 7.94 % Favored : 91.12 % 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: 2.67 (0.50), residues: 281 helix: 2.59 (0.34), residues: 222 sheet: None (None), residues: 0 loop : -1.68 (0.67), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 173 HIS 0.004 0.001 HIS R 296 PHE 0.010 0.001 PHE R 290 TYR 0.010 0.001 TYR R 308 ARG 0.002 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 0.207 Fit side-chains REVERT: R 63 ARG cc_start: 0.8137 (ptp90) cc_final: 0.6309 (mmt90) outliers start: 2 outliers final: 2 residues processed: 24 average time/residue: 0.1251 time to fit residues: 3.7185 Evaluate side-chains 23 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 21 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 20 optimal weight: 0.4980 chunk 19 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 24 optimal weight: 0.0770 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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: 0.8254 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2225 Z= 0.164 Angle : 0.434 5.334 3050 Z= 0.242 Chirality : 0.037 0.122 374 Planarity : 0.003 0.026 366 Dihedral : 4.379 20.157 316 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.87 % Allowed : 9.35 % Favored : 88.79 % 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: 2.98 (0.50), residues: 281 helix: 2.82 (0.34), residues: 223 sheet: None (None), residues: 0 loop : -1.68 (0.68), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 173 HIS 0.003 0.001 HIS R 296 PHE 0.009 0.001 PHE R 108 TYR 0.009 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) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 20 time to evaluate : 0.242 Fit side-chains REVERT: R 63 ARG cc_start: 0.8011 (ptp90) cc_final: 0.6297 (mmt90) REVERT: R 101 PHE cc_start: 0.8351 (m-80) cc_final: 0.8007 (m-80) outliers start: 4 outliers final: 2 residues processed: 23 average time/residue: 0.1373 time to fit residues: 3.9589 Evaluate side-chains 21 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 19 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 0.1980 chunk 18 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 0.0570 chunk 6 optimal weight: 0.7980 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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: 0.8260 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2225 Z= 0.172 Angle : 0.435 5.331 3050 Z= 0.241 Chirality : 0.037 0.121 374 Planarity : 0.003 0.026 366 Dihedral : 4.299 19.680 316 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.34 % Allowed : 10.75 % Favored : 86.92 % 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: 3.06 (0.50), residues: 281 helix: 2.89 (0.34), residues: 223 sheet: None (None), residues: 0 loop : -1.68 (0.68), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 173 HIS 0.003 0.001 HIS R 296 PHE 0.007 0.001 PHE R 290 TYR 0.009 0.001 TYR R 308 ARG 0.001 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 20 time to evaluate : 0.193 Fit side-chains REVERT: R 63 ARG cc_start: 0.7944 (ptp90) cc_final: 0.6271 (mmt90) REVERT: R 101 PHE cc_start: 0.8337 (m-80) cc_final: 0.8034 (m-80) outliers start: 5 outliers final: 5 residues processed: 24 average time/residue: 0.1562 time to fit residues: 4.6103 Evaluate side-chains 25 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 20 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 314 ILE 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: 0.7980 chunk 5 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 27 optimal weight: 0.0070 chunk 22 optimal weight: 0.0980 chunk 12 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 overall best weight: 0.4198 ------------------------------------------------------------------------------- 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: 0.8238 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2225 Z= 0.149 Angle : 0.418 5.291 3050 Z= 0.231 Chirality : 0.037 0.119 374 Planarity : 0.003 0.025 366 Dihedral : 4.186 19.696 316 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.34 % Allowed : 11.21 % Favored : 86.45 % 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: 3.22 (0.50), residues: 281 helix: 2.99 (0.34), residues: 223 sheet: None (None), residues: 0 loop : -1.61 (0.70), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 173 HIS 0.002 0.001 HIS R 296 PHE 0.007 0.001 PHE R 217 TYR 0.009 0.001 TYR R 308 ARG 0.001 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 21 time to evaluate : 0.238 Fit side-chains REVERT: R 63 ARG cc_start: 0.7928 (ptp90) cc_final: 0.6184 (mmt90) REVERT: R 101 PHE cc_start: 0.8348 (m-80) cc_final: 0.8086 (m-80) outliers start: 5 outliers final: 5 residues processed: 25 average time/residue: 0.1453 time to fit residues: 4.4741 Evaluate side-chains 25 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 20 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.8297 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2225 Z= 0.217 Angle : 0.457 5.368 3050 Z= 0.253 Chirality : 0.038 0.121 374 Planarity : 0.003 0.027 366 Dihedral : 4.415 19.583 316 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.80 % Allowed : 11.21 % Favored : 85.98 % 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: 2.97 (0.50), residues: 281 helix: 2.81 (0.34), residues: 223 sheet: None (None), residues: 0 loop : -1.68 (0.70), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 173 HIS 0.003 0.001 HIS R 296 PHE 0.009 0.001 PHE R 290 TYR 0.010 0.001 TYR R 308 ARG 0.001 0.000 ARG R 221 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 19 time to evaluate : 0.217 Fit side-chains REVERT: R 63 ARG cc_start: 0.7946 (ptp90) cc_final: 0.6150 (mmt90) REVERT: R 101 PHE cc_start: 0.8350 (m-80) cc_final: 0.8029 (m-80) outliers start: 6 outliers final: 6 residues processed: 23 average time/residue: 0.1258 time to fit residues: 3.6800 Evaluate side-chains 25 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 19 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 171 MET Chi-restraints excluded: chain R residue 314 ILE 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: 0.6980 chunk 2 optimal weight: 0.4980 chunk 21 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.8290 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2225 Z= 0.198 Angle : 0.445 5.350 3050 Z= 0.247 Chirality : 0.037 0.120 374 Planarity : 0.003 0.028 366 Dihedral : 4.413 19.813 316 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.80 % Allowed : 11.21 % Favored : 85.98 % 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: 2.97 (0.50), residues: 281 helix: 2.85 (0.34), residues: 221 sheet: None (None), residues: 0 loop : -1.69 (0.69), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 173 HIS 0.003 0.001 HIS R 296 PHE 0.008 0.001 PHE R 290 TYR 0.009 0.001 TYR R 308 ARG 0.001 0.000 ARG R 221 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 20 time to evaluate : 0.244 Fit side-chains REVERT: R 63 ARG cc_start: 0.7935 (ptp90) cc_final: 0.6150 (mmt90) REVERT: R 101 PHE cc_start: 0.8362 (m-80) cc_final: 0.8052 (m-80) outliers start: 6 outliers final: 5 residues processed: 25 average time/residue: 0.1473 time to fit residues: 4.5152 Evaluate side-chains 26 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 21 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 314 ILE 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: 0.2980 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.8282 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2225 Z= 0.185 Angle : 0.438 5.327 3050 Z= 0.243 Chirality : 0.037 0.119 374 Planarity : 0.003 0.028 366 Dihedral : 4.358 19.772 316 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.80 % Allowed : 12.15 % Favored : 85.05 % 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: 3.03 (0.50), residues: 281 helix: 2.89 (0.34), residues: 221 sheet: None (None), residues: 0 loop : -1.64 (0.71), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 173 HIS 0.003 0.001 HIS R 296 PHE 0.008 0.001 PHE R 290 TYR 0.009 0.001 TYR R 308 ARG 0.001 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 21 time to evaluate : 0.182 Fit side-chains REVERT: R 63 ARG cc_start: 0.7912 (ptp90) cc_final: 0.6127 (mmt90) outliers start: 6 outliers final: 6 residues processed: 26 average time/residue: 0.1145 time to fit residues: 3.6534 Evaluate side-chains 26 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 20 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 0.2980 chunk 23 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.8288 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2225 Z= 0.192 Angle : 0.441 5.325 3050 Z= 0.244 Chirality : 0.037 0.119 374 Planarity : 0.003 0.028 366 Dihedral : 4.377 19.783 316 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.80 % Allowed : 13.08 % Favored : 84.11 % 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: 2.99 (0.50), residues: 281 helix: 2.82 (0.34), residues: 223 sheet: None (None), residues: 0 loop : -1.64 (0.72), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 173 HIS 0.003 0.001 HIS R 296 PHE 0.010 0.001 PHE R 101 TYR 0.009 0.001 TYR R 308 ARG 0.001 0.000 ARG R 221 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 19 time to evaluate : 0.269 Fit side-chains REVERT: R 63 ARG cc_start: 0.7923 (ptp90) cc_final: 0.6123 (mmt90) outliers start: 6 outliers final: 6 residues processed: 24 average time/residue: 0.1501 time to fit residues: 4.4697 Evaluate side-chains 25 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 19 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 1 optimal weight: 0.0970 chunk 26 optimal weight: 0.0770 chunk 5 optimal weight: 0.9980 overall best weight: 0.4136 ------------------------------------------------------------------------------- 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: 0.8248 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2225 Z= 0.150 Angle : 0.416 5.286 3050 Z= 0.229 Chirality : 0.036 0.116 374 Planarity : 0.003 0.027 366 Dihedral : 4.190 19.827 316 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.80 % Allowed : 13.08 % Favored : 84.11 % 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: 3.19 (0.51), residues: 281 helix: 2.96 (0.34), residues: 223 sheet: None (None), residues: 0 loop : -1.54 (0.74), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 173 HIS 0.002 0.001 HIS R 296 PHE 0.009 0.001 PHE R 101 TYR 0.009 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) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 19 time to evaluate : 0.212 Fit side-chains REVERT: R 63 ARG cc_start: 0.7893 (ptp90) cc_final: 0.6117 (mmt90) outliers start: 6 outliers final: 6 residues processed: 24 average time/residue: 0.1516 time to fit residues: 4.3946 Evaluate side-chains 25 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 19 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 3 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3354 r_free = 0.3354 target = 0.123794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.106904 restraints weight = 2723.967| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.49 r_work: 0.3059 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2225 Z= 0.222 Angle : 0.456 5.366 3050 Z= 0.252 Chirality : 0.038 0.120 374 Planarity : 0.003 0.028 366 Dihedral : 4.422 19.616 316 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.27 % Allowed : 12.62 % Favored : 84.11 % 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: 2.95 (0.50), residues: 281 helix: 2.78 (0.34), residues: 223 sheet: None (None), residues: 0 loop : -1.61 (0.72), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 173 HIS 0.004 0.001 HIS R 296 PHE 0.009 0.001 PHE R 290 TYR 0.010 0.001 TYR R 308 ARG 0.001 0.000 ARG R 221 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 951.59 seconds wall clock time: 17 minutes 51.03 seconds (1071.03 seconds total)