Starting phenix.real_space_refine on Wed Nov 13 23:12:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gh1_40028/11_2024/8gh1_40028.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gh1_40028/11_2024/8gh1_40028.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gh1_40028/11_2024/8gh1_40028.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gh1_40028/11_2024/8gh1_40028.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gh1_40028/11_2024/8gh1_40028.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gh1_40028/11_2024/8gh1_40028.cif" } resolution = 4.1 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= 0.015 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 10 5.16 5 C 1299 2.51 5 N 328 2.21 5 O 339 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 1976 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 1961 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Unresolved non-hydrogen bonds: 303 Unresolved non-hydrogen angles: 385 Unresolved non-hydrogen dihedrals: 234 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 122 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: 3.21, per 1000 atoms: 1.62 Number of scatterers: 1976 At special positions: 0 Unit cell: (55.5328, 86.77, 65.0775, 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 10 16.00 O 339 8.00 N 328 7.00 C 1299 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 256.0 milliseconds 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 538 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 0 sheets defined 85.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'R' and resid 31 through 60 removed outlier: 3.557A pdb=" N GLY R 35 " --> pdb=" O VAL R 31 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL R 48 " --> pdb=" O VAL R 44 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE R 49 " --> pdb=" O LEU R 45 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU R 53 " --> pdb=" O PHE R 49 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 96 removed outlier: 3.686A pdb=" N TYR R 70 " --> pdb=" O THR R 66 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 4.241A 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 105 through 137 removed outlier: 3.602A pdb=" N SER R 137 " --> pdb=" O PHE R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 145 removed outlier: 3.949A pdb=" N GLN R 142 " --> pdb=" O PRO R 138 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER R 143 " --> pdb=" O PHE R 139 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU R 145 " --> pdb=" O TYR R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 171 removed outlier: 3.662A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE R 153 " --> pdb=" O LYS R 149 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE R 154 " --> pdb=" O ALA R 150 " (cutoff:3.500A) Proline residue: R 168 - end of helix removed outlier: 3.516A pdb=" N MET R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 187 Processing helix chain 'R' and resid 196 through 208 removed outlier: 3.575A pdb=" N ALA R 200 " --> pdb=" O ASN R 196 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE R 201 " --> pdb=" O GLN R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 236 removed outlier: 4.037A pdb=" N SER R 236 " --> pdb=" O LYS R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 296 removed outlier: 3.973A pdb=" N THR R 274 " --> pdb=" O LYS R 270 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE R 278 " --> pdb=" O THR R 274 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N CYS R 285 " --> pdb=" O THR R 281 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.710A pdb=" N VAL R 295 " --> pdb=" O ILE R 291 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS R 296 " --> pdb=" O VAL R 292 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 327 removed outlier: 3.682A pdb=" N GLY R 315 " --> pdb=" O LEU R 311 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR R 316 " --> pdb=" O ASN R 312 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 340 removed outlier: 3.523A pdb=" N LEU R 339 " --> pdb=" O ALA R 335 " (cutoff:3.500A) 153 hydrogen bonds defined for protein. 459 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: 0.47 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 621 1.34 - 1.46: 529 1.46 - 1.58: 867 1.58 - 1.69: 0 1.69 - 1.81: 13 Bond restraints: 2030 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.452 -0.055 2.00e-02 2.50e+03 7.45e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.443 -0.049 2.00e-02 2.50e+03 6.00e+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 5.48e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.567 -0.047 2.00e-02 2.50e+03 5.43e+00 bond pdb=" CAE G1I R 501 " pdb=" CAG G1I R 501 " ideal model delta sigma weight residual 1.506 1.539 -0.033 2.00e-02 2.50e+03 2.66e+00 ... (remaining 2025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 2664 1.12 - 2.23: 105 2.23 - 3.35: 11 3.35 - 4.47: 5 4.47 - 5.58: 9 Bond angle restraints: 2794 Sorted by residual: angle pdb=" C GLU R 107 " pdb=" N PHE R 108 " pdb=" CA PHE R 108 " ideal model delta sigma weight residual 121.58 116.26 5.32 1.95e+00 2.63e-01 7.44e+00 angle pdb=" N TYR R 326 " pdb=" CA TYR R 326 " pdb=" C TYR R 326 " ideal model delta sigma weight residual 111.36 114.23 -2.87 1.09e+00 8.42e-01 6.92e+00 angle pdb=" CAE G1I R 501 " pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 112.63 117.66 -5.03 3.00e+00 1.11e-01 2.81e+00 angle pdb=" CA LEU R 230 " pdb=" CB LEU R 230 " pdb=" CG LEU R 230 " ideal model delta sigma weight residual 116.30 121.88 -5.58 3.50e+00 8.16e-02 2.54e+00 angle pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " pdb=" CAI G1I R 501 " ideal model delta sigma weight residual 110.89 115.56 -4.67 3.00e+00 1.11e-01 2.42e+00 ... (remaining 2789 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.96: 1028 14.96 - 29.91: 93 29.91 - 44.87: 19 44.87 - 59.82: 3 59.82 - 74.78: 3 Dihedral angle restraints: 1146 sinusoidal: 318 harmonic: 828 Sorted by residual: dihedral pdb=" CB CYS R 184 " pdb=" SG CYS R 184 " pdb=" SG CYS R 190 " pdb=" CB CYS R 190 " ideal model delta sinusoidal sigma weight residual 93.00 167.78 -74.78 1 1.00e+01 1.00e-02 7.08e+01 dihedral pdb=" CA ILE R 277 " pdb=" C ILE R 277 " pdb=" N ILE R 278 " pdb=" CA ILE R 278 " ideal model delta harmonic sigma weight residual -180.00 -162.43 -17.57 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA ASP R 234 " pdb=" CB ASP R 234 " pdb=" CG ASP R 234 " pdb=" OD1 ASP R 234 " ideal model delta sinusoidal sigma weight residual -30.00 -85.10 55.10 1 2.00e+01 2.50e-03 1.03e+01 ... (remaining 1143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 213 0.035 - 0.070: 99 0.070 - 0.105: 17 0.105 - 0.140: 1 0.140 - 0.174: 1 Chirality restraints: 331 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.57 -0.17 2.00e-01 2.50e+01 7.61e-01 chirality pdb=" CA PHE R 108 " pdb=" N PHE R 108 " pdb=" C PHE R 108 " pdb=" CB PHE R 108 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.39e-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 0.10 2.00e-01 2.50e+01 2.74e-01 ... (remaining 328 not shown) Planarity restraints: 351 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR R 283 " 0.004 2.00e-02 2.50e+03 8.55e-03 7.32e-01 pdb=" C THR R 283 " -0.015 2.00e-02 2.50e+03 pdb=" O THR R 283 " 0.006 2.00e-02 2.50e+03 pdb=" N LEU R 284 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER R 137 " 0.014 5.00e-02 4.00e+02 2.13e-02 7.24e-01 pdb=" N PRO R 138 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO R 138 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO R 138 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP R 109 " 0.004 2.00e-02 2.50e+03 8.40e-03 7.05e-01 pdb=" C TRP R 109 " -0.015 2.00e-02 2.50e+03 pdb=" O TRP R 109 " 0.005 2.00e-02 2.50e+03 pdb=" N THR R 110 " 0.005 2.00e-02 2.50e+03 ... (remaining 348 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 451 2.78 - 3.31: 2008 3.31 - 3.84: 3205 3.84 - 4.37: 2963 4.37 - 4.90: 5438 Nonbonded interactions: 14065 Sorted by model distance: nonbonded pdb=" OD1 ASP R 113 " pdb=" OAM G1I R 501 " model vdw 2.249 3.040 nonbonded pdb=" O SER R 236 " pdb=" OG SER R 236 " model vdw 2.508 3.040 nonbonded pdb=" OD2 ASP R 113 " pdb=" OH TYR R 316 " model vdw 2.522 3.040 nonbonded pdb=" O GLU R 107 " pdb=" OG1 THR R 110 " model vdw 2.524 3.040 nonbonded pdb=" O TYR R 70 " pdb=" OG1 THR R 73 " model vdw 2.541 3.040 ... (remaining 14060 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 group one per residue 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: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.780 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 2030 Z= 0.223 Angle : 0.570 5.584 2794 Z= 0.294 Chirality : 0.040 0.174 331 Planarity : 0.003 0.025 351 Dihedral : 12.639 70.305 605 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.52), residues: 277 helix: 1.88 (0.38), residues: 204 sheet: None (None), residues: 0 loop : -1.28 (0.71), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 158 HIS 0.003 0.001 HIS R 93 PHE 0.011 0.001 PHE R 108 TYR 0.005 0.001 TYR R 308 ARG 0.007 0.001 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.204 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1232 time to fit residues: 6.1773 Evaluate side-chains 32 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 0.7980 chunk 21 optimal weight: 0.0270 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2030 Z= 0.194 Angle : 0.544 5.250 2794 Z= 0.296 Chirality : 0.039 0.131 331 Planarity : 0.004 0.026 351 Dihedral : 4.927 15.765 310 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.52), residues: 277 helix: 1.91 (0.37), residues: 207 sheet: None (None), residues: 0 loop : -0.75 (0.71), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 109 HIS 0.003 0.001 HIS R 93 PHE 0.022 0.002 PHE R 332 TYR 0.008 0.001 TYR R 326 ARG 0.005 0.001 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.214 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1013 time to fit residues: 6.3464 Evaluate side-chains 32 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2030 Z= 0.206 Angle : 0.526 5.186 2794 Z= 0.288 Chirality : 0.039 0.117 331 Planarity : 0.003 0.028 351 Dihedral : 4.749 16.190 310 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % 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: 1.88 (0.50), residues: 277 helix: 2.14 (0.37), residues: 198 sheet: None (None), residues: 0 loop : -1.14 (0.63), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 158 HIS 0.003 0.002 HIS R 296 PHE 0.019 0.002 PHE R 108 TYR 0.007 0.001 TYR R 199 ARG 0.006 0.001 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.223 Fit side-chains REVERT: R 174 TYR cc_start: 0.8210 (p90) cc_final: 0.7751 (p90) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1082 time to fit residues: 6.1901 Evaluate side-chains 32 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 0.0980 chunk 6 optimal weight: 2.9990 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: 0.7889 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2030 Z= 0.178 Angle : 0.530 5.283 2794 Z= 0.285 Chirality : 0.038 0.130 331 Planarity : 0.003 0.030 351 Dihedral : 4.555 15.356 310 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.51), residues: 277 helix: 2.17 (0.37), residues: 198 sheet: None (None), residues: 0 loop : -1.22 (0.64), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 158 HIS 0.003 0.001 HIS R 93 PHE 0.027 0.002 PHE R 332 TYR 0.006 0.001 TYR R 199 ARG 0.006 0.001 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.220 Fit side-chains REVERT: R 174 TYR cc_start: 0.8223 (p90) cc_final: 0.7989 (p90) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1243 time to fit residues: 7.3558 Evaluate side-chains 33 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 0.0030 chunk 5 optimal weight: 0.0970 chunk 15 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 2 optimal weight: 0.0070 chunk 8 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 overall best weight: 0.2806 ------------------------------------------------------------------------------- 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: 0.7815 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2030 Z= 0.137 Angle : 0.507 5.163 2794 Z= 0.266 Chirality : 0.037 0.123 331 Planarity : 0.004 0.029 351 Dihedral : 4.237 15.089 310 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.52), residues: 277 helix: 2.37 (0.37), residues: 198 sheet: None (None), residues: 0 loop : -1.18 (0.66), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 109 HIS 0.004 0.001 HIS R 93 PHE 0.013 0.001 PHE R 108 TYR 0.005 0.001 TYR R 308 ARG 0.007 0.001 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.229 Fit side-chains REVERT: R 174 TYR cc_start: 0.8181 (p90) cc_final: 0.7775 (p90) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1071 time to fit residues: 6.4102 Evaluate side-chains 32 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 22 optimal weight: 0.0980 chunk 16 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7863 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2030 Z= 0.183 Angle : 0.532 5.253 2794 Z= 0.282 Chirality : 0.038 0.109 331 Planarity : 0.003 0.030 351 Dihedral : 4.259 15.699 310 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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: 2.12 (0.51), residues: 277 helix: 2.35 (0.37), residues: 198 sheet: None (None), residues: 0 loop : -1.14 (0.67), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 158 HIS 0.004 0.001 HIS R 172 PHE 0.030 0.002 PHE R 332 TYR 0.005 0.001 TYR R 199 ARG 0.007 0.001 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.211 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1034 time to fit residues: 6.4037 Evaluate side-chains 32 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 0.0370 chunk 13 optimal weight: 0.5980 chunk 2 optimal weight: 0.0970 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 0.0070 chunk 25 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 overall best weight: 0.2674 ------------------------------------------------------------------------------- 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: 0.7808 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2030 Z= 0.145 Angle : 0.504 5.762 2794 Z= 0.262 Chirality : 0.037 0.106 331 Planarity : 0.003 0.029 351 Dihedral : 4.049 14.874 310 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.51), residues: 277 helix: 2.44 (0.37), residues: 198 sheet: None (None), residues: 0 loop : -1.26 (0.65), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 158 HIS 0.004 0.001 HIS R 93 PHE 0.015 0.001 PHE R 108 TYR 0.018 0.001 TYR R 174 ARG 0.006 0.001 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.240 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1099 time to fit residues: 6.7879 Evaluate side-chains 33 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 0.0970 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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: 0.7851 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2030 Z= 0.168 Angle : 0.536 6.702 2794 Z= 0.281 Chirality : 0.038 0.107 331 Planarity : 0.003 0.029 351 Dihedral : 4.140 15.504 310 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.51), residues: 277 helix: 2.37 (0.37), residues: 198 sheet: None (None), residues: 0 loop : -1.32 (0.64), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 158 HIS 0.003 0.001 HIS R 93 PHE 0.033 0.002 PHE R 332 TYR 0.005 0.001 TYR R 199 ARG 0.006 0.001 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.219 Fit side-chains REVERT: R 174 TYR cc_start: 0.8053 (p90) cc_final: 0.7850 (p90) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1001 time to fit residues: 6.3484 Evaluate side-chains 32 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 6 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 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: 0.7887 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2030 Z= 0.184 Angle : 0.559 6.072 2794 Z= 0.293 Chirality : 0.039 0.115 331 Planarity : 0.003 0.031 351 Dihedral : 4.214 15.173 310 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.51), residues: 277 helix: 2.20 (0.37), residues: 201 sheet: None (None), residues: 0 loop : -1.16 (0.66), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 158 HIS 0.003 0.001 HIS R 93 PHE 0.018 0.002 PHE R 336 TYR 0.006 0.001 TYR R 199 ARG 0.006 0.001 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.220 Fit side-chains REVERT: R 174 TYR cc_start: 0.8109 (p90) cc_final: 0.7900 (p90) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1046 time to fit residues: 5.9970 Evaluate side-chains 38 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.7936 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2030 Z= 0.208 Angle : 0.590 6.413 2794 Z= 0.309 Chirality : 0.039 0.111 331 Planarity : 0.004 0.030 351 Dihedral : 4.408 16.089 310 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.50), residues: 277 helix: 2.02 (0.36), residues: 201 sheet: None (None), residues: 0 loop : -1.11 (0.67), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 158 HIS 0.003 0.001 HIS R 93 PHE 0.016 0.002 PHE R 166 TYR 0.006 0.001 TYR R 199 ARG 0.006 0.001 ARG R 131 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.197 Fit side-chains REVERT: R 174 TYR cc_start: 0.8227 (p90) cc_final: 0.7855 (p90) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1003 time to fit residues: 6.3649 Evaluate side-chains 34 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.3980 chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 0.0870 chunk 0 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 2 optimal weight: 0.4980 chunk 7 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 18 optimal weight: 0.2980 chunk 9 optimal weight: 0.9990 overall best weight: 0.3958 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.141555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.126216 restraints weight = 4636.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.128836 restraints weight = 2699.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.130590 restraints weight = 1779.650| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2030 Z= 0.152 Angle : 0.543 5.847 2794 Z= 0.284 Chirality : 0.038 0.112 331 Planarity : 0.004 0.029 351 Dihedral : 4.172 15.417 310 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.50), residues: 277 helix: 2.15 (0.37), residues: 201 sheet: None (None), residues: 0 loop : -1.18 (0.65), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 158 HIS 0.003 0.001 HIS R 93 PHE 0.028 0.002 PHE R 332 TYR 0.005 0.001 TYR R 308 ARG 0.006 0.001 ARG R 131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 901.00 seconds wall clock time: 21 minutes 52.59 seconds (1312.59 seconds total)