Starting phenix.real_space_refine on Thu Jul 18 17:29:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggn_40014/07_2024/8ggn_40014.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggn_40014/07_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_40014/07_2024/8ggn_40014.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggn_40014/07_2024/8ggn_40014.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggn_40014/07_2024/8ggn_40014.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggn_40014/07_2024/8ggn_40014.cif" } 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-5388/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: 2.42, per 1000 atoms: 1.12 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: 1.77 Conformation dependent library (CDL) restraints added in 477.8 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... Secondary structure from input PDB file: 12 helices and 0 sheets defined 88.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'R' and resid 31 through 61 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) removed outlier: 3.559A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 97 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 102 through 137 removed outlier: 3.640A pdb=" N CYS R 106 " --> pdb=" O GLY R 102 " (cutoff:3.500A) 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 140 through 145 Processing helix chain 'R' and resid 146 through 171 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 removed outlier: 3.583A pdb=" N MET R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 208 Processing helix chain 'R' and resid 208 through 237 Processing helix chain 'R' and resid 270 through 299 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 304 through 317 removed outlier: 3.567A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 327 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 329 through 340 168 hydrogen bonds defined for protein. 504 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: 0.55 Time building geometry restraints manager: 0.89 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: 2101 3.31 - 3.84: 3495 3.84 - 4.37: 3607 4.37 - 4.90: 6804 Nonbonded interactions: 16479 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 16474 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 12.710 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.170 ------------------------------------------------------------------------------- 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= 0.319 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 : 0.227 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1759 time to fit residues: 4.8263 Evaluate side-chains 18 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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: 0.5980 chunk 7 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.0882 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= 0.225 Angle : 0.489 5.552 3050 Z= 0.277 Chirality : 0.038 0.127 374 Planarity : 0.003 0.027 366 Dihedral : 4.756 20.510 316 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.93 % Allowed : 7.48 % Favored : 91.59 % 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: 2.70 (0.49), residues: 281 helix: 2.58 (0.33), residues: 224 sheet: None (None), residues: 0 loop : -1.68 (0.68), residues: 57 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 108 TYR 0.010 0.001 TYR R 199 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 25 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.238 Fit side-chains REVERT: R 63 ARG cc_start: 0.8170 (ptp90) cc_final: 0.6321 (mmt90) outliers start: 2 outliers final: 1 residues processed: 25 average time/residue: 0.1704 time to fit residues: 5.0352 Evaluate side-chains 21 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 25 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 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: 0.8282 moved from start: 0.1131 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= 0.227 Angle : 0.484 5.411 3050 Z= 0.268 Chirality : 0.038 0.125 374 Planarity : 0.003 0.028 366 Dihedral : 4.554 20.722 316 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.80 % Allowed : 9.35 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.49), residues: 281 helix: 2.71 (0.33), residues: 224 sheet: None (None), residues: 0 loop : -1.78 (0.67), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 173 HIS 0.004 0.001 HIS R 296 PHE 0.009 0.001 PHE R 290 TYR 0.009 0.001 TYR R 199 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 26 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 20 time to evaluate : 0.237 Fit side-chains REVERT: R 63 ARG cc_start: 0.8017 (ptp90) cc_final: 0.6267 (mmt90) REVERT: R 101 PHE cc_start: 0.8398 (m-80) cc_final: 0.8062 (m-80) outliers start: 6 outliers final: 4 residues processed: 24 average time/residue: 0.1435 time to fit residues: 4.2558 Evaluate side-chains 24 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 20 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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 165 SER 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: 4.9990 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 23 optimal weight: 0.4980 chunk 18 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 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: 0.8294 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2225 Z= 0.236 Angle : 0.481 5.381 3050 Z= 0.268 Chirality : 0.038 0.124 374 Planarity : 0.003 0.028 366 Dihedral : 4.540 20.605 316 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.34 % Allowed : 11.68 % 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: 2.87 (0.49), residues: 281 helix: 2.73 (0.33), residues: 224 sheet: None (None), residues: 0 loop : -1.74 (0.67), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 199 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 26 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 21 time to evaluate : 0.184 Fit side-chains REVERT: R 63 ARG cc_start: 0.7948 (ptp90) cc_final: 0.6224 (mmt90) REVERT: R 101 PHE cc_start: 0.8355 (m-80) cc_final: 0.7993 (m-80) outliers start: 5 outliers final: 5 residues processed: 25 average time/residue: 0.1646 time to fit residues: 4.8484 Evaluate side-chains 26 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 21 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 163 LEU 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: 0.9980 chunk 24 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 2 optimal weight: 0.3980 chunk 8 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1368 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= 0.229 Angle : 0.473 5.367 3050 Z= 0.265 Chirality : 0.038 0.122 374 Planarity : 0.003 0.029 366 Dihedral : 4.501 20.788 316 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 2.12 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: 2.91 (0.49), residues: 281 helix: 2.75 (0.33), residues: 224 sheet: None (None), residues: 0 loop : -1.70 (0.68), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 173 HIS 0.004 0.001 HIS R 296 PHE 0.009 0.001 PHE R 290 TYR 0.009 0.001 TYR R 199 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 27 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 21 time to evaluate : 0.237 Fit side-chains REVERT: R 63 ARG cc_start: 0.7942 (ptp90) cc_final: 0.6162 (mmt90) REVERT: R 101 PHE cc_start: 0.8373 (m-80) cc_final: 0.8040 (m-80) outliers start: 6 outliers final: 5 residues processed: 26 average time/residue: 0.1856 time to fit residues: 5.7193 Evaluate side-chains 26 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 21 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 163 LEU 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: 0.9980 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 10 optimal weight: 0.1980 chunk 8 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 17 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: 0.8269 moved from start: 0.1435 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= 0.199 Angle : 0.453 5.324 3050 Z= 0.253 Chirality : 0.037 0.122 374 Planarity : 0.003 0.028 366 Dihedral : 4.378 20.742 316 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.34 % Allowed : 12.62 % 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: 3.06 (0.50), residues: 281 helix: 2.87 (0.34), residues: 224 sheet: None (None), residues: 0 loop : -1.69 (0.70), residues: 57 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 199 ARG 0.001 0.000 ARG R 63 *********************** 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: 5 poor density : 20 time to evaluate : 0.228 Fit side-chains REVERT: R 63 ARG cc_start: 0.7918 (ptp90) cc_final: 0.6153 (mmt90) REVERT: R 101 PHE cc_start: 0.8359 (m-80) cc_final: 0.8071 (m-80) outliers start: 5 outliers final: 5 residues processed: 24 average time/residue: 0.1372 time to fit residues: 4.0963 Evaluate side-chains 24 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 19 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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 163 LEU 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: 0.6980 chunk 13 optimal weight: 0.3980 chunk 2 optimal weight: 0.0670 chunk 21 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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: 0.1505 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= 0.176 Angle : 0.440 5.299 3050 Z= 0.244 Chirality : 0.037 0.119 374 Planarity : 0.003 0.027 366 Dihedral : 4.262 20.700 316 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.27 % Allowed : 12.15 % Favored : 84.58 % 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: 3.16 (0.50), residues: 281 helix: 2.92 (0.34), residues: 225 sheet: None (None), residues: 0 loop : -1.68 (0.71), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 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 199 ARG 0.001 0.000 ARG R 63 *********************** 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 27 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 20 time to evaluate : 0.240 Fit side-chains REVERT: R 63 ARG cc_start: 0.7896 (ptp90) cc_final: 0.6146 (mmt90) REVERT: R 101 PHE cc_start: 0.8319 (m-80) cc_final: 0.8116 (m-80) outliers start: 7 outliers final: 6 residues processed: 26 average time/residue: 0.1282 time to fit residues: 4.1638 Evaluate side-chains 26 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 20 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 0.1980 chunk 26 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 2 optimal weight: 0.0570 chunk 17 optimal weight: 0.0870 chunk 13 optimal weight: 0.6980 overall best weight: 0.3076 ------------------------------------------------------------------------------- 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: 0.8187 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2225 Z= 0.136 Angle : 0.414 5.247 3050 Z= 0.228 Chirality : 0.036 0.115 374 Planarity : 0.003 0.026 366 Dihedral : 4.041 20.449 316 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.34 % Allowed : 13.08 % Favored : 84.58 % 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: 3.38 (0.51), residues: 281 helix: 3.09 (0.34), residues: 225 sheet: None (None), residues: 0 loop : -1.66 (0.71), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 173 HIS 0.001 0.001 HIS R 296 PHE 0.007 0.001 PHE R 108 TYR 0.007 0.001 TYR R 308 ARG 0.001 0.000 ARG R 63 *********************** 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 25 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 20 time to evaluate : 0.180 Fit side-chains REVERT: R 63 ARG cc_start: 0.7845 (ptp90) cc_final: 0.6165 (mmt90) outliers start: 5 outliers final: 4 residues processed: 23 average time/residue: 0.1323 time to fit residues: 3.7210 Evaluate side-chains 23 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 19 time to evaluate : 0.186 ------------------------------------------------------------------------------- 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 314 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 0.5980 chunk 23 optimal weight: 0.0980 chunk 6 optimal weight: 0.7980 chunk 20 optimal weight: 0.1980 chunk 3 optimal weight: 0.0170 chunk 22 optimal weight: 0.4980 chunk 9 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 overall best weight: 0.2818 ------------------------------------------------------------------------------- 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: 0.8174 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2225 Z= 0.131 Angle : 0.411 5.246 3050 Z= 0.225 Chirality : 0.036 0.113 374 Planarity : 0.003 0.025 366 Dihedral : 3.978 20.188 316 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 2.80 % Allowed : 13.55 % Favored : 83.64 % 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: 3.43 (0.50), residues: 281 helix: 3.06 (0.34), residues: 227 sheet: None (None), residues: 0 loop : -1.48 (0.70), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 173 HIS 0.001 0.000 HIS R 296 PHE 0.013 0.001 PHE R 101 TYR 0.008 0.001 TYR R 199 ARG 0.001 0.000 ARG R 63 *********************** 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 26 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 20 time to evaluate : 0.235 Fit side-chains REVERT: R 63 ARG cc_start: 0.7834 (ptp90) cc_final: 0.6150 (mmt90) outliers start: 6 outliers final: 4 residues processed: 23 average time/residue: 0.1281 time to fit residues: 3.6498 Evaluate side-chains 23 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 19 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 135 ILE 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: 1.9990 chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 chunk 5 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.8296 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2225 Z= 0.260 Angle : 0.480 5.402 3050 Z= 0.268 Chirality : 0.039 0.122 374 Planarity : 0.003 0.026 366 Dihedral : 4.464 20.121 316 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 2.34 % Allowed : 14.49 % Favored : 83.18 % 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: 3.01 (0.49), residues: 281 helix: 2.78 (0.33), residues: 225 sheet: None (None), residues: 0 loop : -1.56 (0.69), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 173 HIS 0.004 0.001 HIS R 296 PHE 0.010 0.001 PHE R 101 TYR 0.011 0.001 TYR R 308 ARG 0.001 0.000 ARG R 175 ********************** 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: 5 poor density : 20 time to evaluate : 0.313 Fit side-chains REVERT: R 63 ARG cc_start: 0.7945 (ptp90) cc_final: 0.6127 (mmt90) outliers start: 5 outliers final: 5 residues processed: 24 average time/residue: 0.1745 time to fit residues: 5.0813 Evaluate side-chains 25 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 20 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 VAL 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: 1.9990 chunk 5 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 0.0970 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 0.0980 chunk 2 optimal weight: 0.1980 chunk 7 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 18 optimal weight: 0.0870 chunk 9 optimal weight: 0.6980 overall best weight: 0.2356 ------------------------------------------------------------------------------- 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 = 0.3450 r_free = 0.3450 target = 0.132196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.115553 restraints weight = 2704.236| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.49 r_work: 0.3176 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2225 Z= 0.124 Angle : 0.406 5.289 3050 Z= 0.223 Chirality : 0.036 0.114 374 Planarity : 0.003 0.024 366 Dihedral : 4.048 20.229 316 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.34 % Allowed : 14.02 % Favored : 83.64 % 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: 3.45 (0.50), residues: 281 helix: 3.16 (0.34), residues: 224 sheet: None (None), residues: 0 loop : -1.66 (0.69), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 173 HIS 0.001 0.000 HIS R 172 PHE 0.012 0.001 PHE R 101 TYR 0.007 0.001 TYR R 308 ARG 0.001 0.000 ARG R 131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 894.84 seconds wall clock time: 19 minutes 59.34 seconds (1199.34 seconds total)