Starting phenix.real_space_refine on Sun Mar 10 18:07:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7srq_25401/03_2024/7srq_25401_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7srq_25401/03_2024/7srq_25401.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7srq_25401/03_2024/7srq_25401.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7srq_25401/03_2024/7srq_25401.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7srq_25401/03_2024/7srq_25401_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7srq_25401/03_2024/7srq_25401_updated.pdb" } resolution = 2.7 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1855 atoms to isotropic. 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 14 5.16 5 C 1323 2.51 5 N 295 2.21 5 O 328 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ASP 135": "OD1" <-> "OD2" Residue "R PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 1960 Number of models: 1 Model: "" Number of chains: 1 Chain: "R" Number of atoms: 1960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1960 Unusual residues: {'7LD': 1, 'NAG': 1} Classifications: {'peptide': 254, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 12, 'TRANS': 241, None: 2} Not linked: pdbres="TYR R 394 " pdbres="NAG R 501 " Not linked: pdbres="NAG R 501 " pdbres="7LD R 502 " Chain breaks: 2 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Time building chain proxies: 1.74, per 1000 atoms: 0.89 Number of scatterers: 1960 At special positions: 0 Unit cell: (51.1943, 56.4005, 75.4899, 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 14 16.00 O 328 8.00 N 295 7.00 C 1323 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 128 " - pdb=" SG CYS R 207 " distance=2.03 Simple disulfide: pdb=" SG CYS R 350 " - pdb=" SG CYS R 353 " 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 Links applied NAG-ASN " NAG R 501 " - " ASN R 204 " Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 354.4 milliseconds 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 486 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 12 helices and 0 sheets defined 78.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'R' and resid 57 through 81 Proline residue: R 67 - end of helix removed outlier: 3.686A pdb=" N ASN R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 116 removed outlier: 3.747A pdb=" N PHE R 92 " --> pdb=" O ALA R 88 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU R 93 " --> pdb=" O THR R 89 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER R 95 " --> pdb=" O TYR R 91 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU R 96 " --> pdb=" O PHE R 92 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N MET R 108 " --> pdb=" O GLY R 104 " (cutoff:3.500A) Proline residue: R 109 - end of helix Processing helix chain 'R' and resid 125 through 157 Proline residue: R 129 - end of helix removed outlier: 4.656A pdb=" N PHE R 138 " --> pdb=" O ASP R 135 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N SER R 139 " --> pdb=" O VAL R 136 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR R 140 " --> pdb=" O LEU R 137 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TRP R 144 " --> pdb=" O ALA R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 169 through 187 Processing helix chain 'R' and resid 189 through 192 No H-bonds generated for 'chain 'R' and resid 189 through 192' Processing helix chain 'R' and resid 202 through 204 No H-bonds generated for 'chain 'R' and resid 202 through 204' Processing helix chain 'R' and resid 216 through 225 Processing helix chain 'R' and resid 227 through 241 removed outlier: 3.616A pdb=" N PHE R 238 " --> pdb=" O ILE R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 324 through 332 removed outlier: 3.673A pdb=" N VAL R 329 " --> pdb=" O VAL R 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 334 through 349 Proline residue: R 339 - end of helix removed outlier: 3.699A pdb=" N ILE R 342 " --> pdb=" O PRO R 339 " (cutoff:3.500A) Processing helix chain 'R' and resid 355 through 381 removed outlier: 3.543A pdb=" N MET R 360 " --> pdb=" O THR R 356 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU R 361 " --> pdb=" O THR R 357 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TRP R 367 " --> pdb=" O GLU R 363 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE R 368 " --> pdb=" O ILE R 364 " (cutoff:3.500A) Proline residue: R 377 - end of helix Processing helix chain 'R' and resid 385 through 393 removed outlier: 3.755A pdb=" N GLY R 392 " --> pdb=" O ARG R 388 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG R 393 " --> pdb=" O ASP R 389 " (cutoff:3.500A) 120 hydrogen bonds defined for protein. 264 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: 0.46 Time building geometry restraints manager: 0.85 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: 567 1.34 - 1.46: 441 1.46 - 1.58: 984 1.58 - 1.69: 0 1.69 - 1.81: 22 Bond restraints: 2014 Sorted by residual: bond pdb=" C14 7LD R 502 " pdb=" C16 7LD R 502 " ideal model delta sigma weight residual 1.525 1.402 0.123 2.00e-02 2.50e+03 3.75e+01 bond pdb=" C11 7LD R 502 " pdb=" C9 7LD R 502 " ideal model delta sigma weight residual 1.525 1.406 0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" C10 7LD R 502 " pdb=" C14 7LD R 502 " ideal model delta sigma weight residual 1.501 1.397 0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" C15 7LD R 502 " pdb=" C7 7LD R 502 " ideal model delta sigma weight residual 1.491 1.396 0.095 2.00e-02 2.50e+03 2.27e+01 bond pdb=" C3 7LD R 502 " pdb=" C7 7LD R 502 " ideal model delta sigma weight residual 1.414 1.322 0.092 2.00e-02 2.50e+03 2.11e+01 ... (remaining 2009 not shown) Histogram of bond angle deviations from ideal: 100.02 - 106.86: 64 106.86 - 113.70: 1170 113.70 - 120.55: 852 120.55 - 127.39: 653 127.39 - 134.23: 28 Bond angle restraints: 2767 Sorted by residual: angle pdb=" CA LEU R 334 " pdb=" C LEU R 334 " pdb=" O LEU R 334 " ideal model delta sigma weight residual 120.90 116.80 4.10 1.07e+00 8.73e-01 1.47e+01 angle pdb=" CA PHE R 331 " pdb=" CB PHE R 331 " pdb=" CG PHE R 331 " ideal model delta sigma weight residual 113.80 117.51 -3.71 1.00e+00 1.00e+00 1.37e+01 angle pdb=" CA LEU R 326 " pdb=" C LEU R 326 " pdb=" O LEU R 326 " ideal model delta sigma weight residual 120.80 117.09 3.71 1.05e+00 9.07e-01 1.25e+01 angle pdb=" N TRP R 337 " pdb=" CA TRP R 337 " pdb=" C TRP R 337 " ideal model delta sigma weight residual 113.50 109.42 4.08 1.23e+00 6.61e-01 1.10e+01 angle pdb=" CA PHE R 330 " pdb=" CB PHE R 330 " pdb=" CG PHE R 330 " ideal model delta sigma weight residual 113.80 116.95 -3.15 1.00e+00 1.00e+00 9.92e+00 ... (remaining 2762 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.36: 1153 30.36 - 60.72: 24 60.72 - 91.08: 4 91.08 - 121.45: 0 121.45 - 151.81: 1 Dihedral angle restraints: 1182 sinusoidal: 438 harmonic: 744 Sorted by residual: dihedral pdb=" CB CYS R 128 " pdb=" SG CYS R 128 " pdb=" SG CYS R 207 " pdb=" CB CYS R 207 " ideal model delta sinusoidal sigma weight residual -86.00 -150.42 64.42 1 1.00e+01 1.00e-02 5.46e+01 dihedral pdb=" C16 7LD R 502 " pdb=" C17 7LD R 502 " pdb=" N3 7LD R 502 " pdb=" C18 7LD R 502 " ideal model delta sinusoidal sigma weight residual 91.75 -116.44 -151.81 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" CA PHE R 117 " pdb=" C PHE R 117 " pdb=" N GLU R 118 " pdb=" CA GLU R 118 " ideal model delta harmonic sigma weight residual -180.00 -161.79 -18.21 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 1179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 303 0.066 - 0.132: 37 0.132 - 0.198: 6 0.198 - 0.263: 0 0.263 - 0.329: 2 Chirality restraints: 348 Sorted by residual: chirality pdb=" C14 7LD R 502 " pdb=" C10 7LD R 502 " pdb=" C13 7LD R 502 " pdb=" C16 7LD R 502 " both_signs ideal model delta sigma weight residual False 2.63 2.30 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" C11 7LD R 502 " pdb=" C15 7LD R 502 " pdb=" C9 7LD R 502 " pdb=" N2 7LD R 502 " both_signs ideal model delta sigma weight residual False 2.48 2.18 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CA PHE R 333 " pdb=" N PHE R 333 " pdb=" C PHE R 333 " pdb=" CB PHE R 333 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.73e-01 ... (remaining 345 not shown) Planarity restraints: 326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE R 188 " 0.042 5.00e-02 4.00e+02 6.39e-02 6.53e+00 pdb=" N PRO R 189 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO R 189 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO R 189 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 370 " 0.014 2.00e-02 2.50e+03 1.24e-02 3.08e+00 pdb=" CG TYR R 370 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR R 370 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR R 370 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR R 370 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR R 370 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR R 370 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR R 370 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 337 " 0.016 2.00e-02 2.50e+03 1.09e-02 2.99e+00 pdb=" CG TRP R 337 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP R 337 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP R 337 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP R 337 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP R 337 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP R 337 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 337 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 337 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP R 337 " -0.002 2.00e-02 2.50e+03 ... (remaining 323 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 562 2.82 - 3.34: 2089 3.34 - 3.86: 3073 3.86 - 4.38: 3435 4.38 - 4.90: 5936 Nonbonded interactions: 15095 Sorted by model distance: nonbonded pdb=" O CYS R 147 " pdb=" OG SER R 150 " model vdw 2.296 2.440 nonbonded pdb=" O PHE R 92 " pdb=" OG SER R 95 " model vdw 2.416 2.440 nonbonded pdb=" O ILE R 174 " pdb=" OG1 THR R 177 " model vdw 2.572 2.440 nonbonded pdb=" O ILE R 155 " pdb=" N LYS R 159 " model vdw 2.573 2.520 nonbonded pdb=" C10 7LD R 502 " pdb=" O1 7LD R 502 " model vdw 2.580 2.672 ... (remaining 15090 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 8.920 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.770 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 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 : 0.008 0.123 2014 Z= 0.462 Angle : 0.801 7.824 2767 Z= 0.467 Chirality : 0.051 0.329 348 Planarity : 0.006 0.064 325 Dihedral : 14.144 151.807 690 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.50 % Allowed : 0.00 % Favored : 98.50 % 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: 0.29 (0.52), residues: 248 helix: 0.73 (0.37), residues: 189 sheet: None (None), residues: 0 loop : -1.36 (0.76), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 337 HIS 0.005 0.002 HIS R 145 PHE 0.020 0.001 PHE R 331 TYR 0.030 0.002 TYR R 370 ARG 0.000 0.000 ARG R 213 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: R 331 PHE cc_start: 0.7019 (OUTLIER) cc_final: 0.6771 (p90) outliers start: 3 outliers final: 2 residues processed: 55 average time/residue: 0.4027 time to fit residues: 23.3525 Evaluate side-chains 46 residues out of total 222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 330 PHE Chi-restraints excluded: chain R residue 331 PHE Chi-restraints excluded: chain R residue 335 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 0.0970 chunk 18 optimal weight: 0.0870 chunk 10 optimal weight: 0.2980 chunk 6 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 0.4980 chunk 7 optimal weight: 0.3980 chunk 11 optimal weight: 0.0980 chunk 14 optimal weight: 0.0470 chunk 22 optimal weight: 0.0870 chunk 15 optimal weight: 0.2980 overall best weight: 0.0832 ------------------------------------------------------------------------------- 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: 0.6924 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 2014 Z= 0.159 Angle : 0.589 6.792 2767 Z= 0.285 Chirality : 0.041 0.180 348 Planarity : 0.005 0.047 325 Dihedral : 11.188 135.365 312 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 4.00 % Allowed : 13.00 % Favored : 83.00 % 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: 0.49 (0.52), residues: 248 helix: 0.77 (0.37), residues: 189 sheet: None (None), residues: 0 loop : -0.88 (0.78), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 180 HIS 0.005 0.002 HIS R 145 PHE 0.015 0.001 PHE R 331 TYR 0.027 0.002 TYR R 370 ARG 0.002 0.001 ARG R 153 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 47 time to evaluate : 0.221 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 50 average time/residue: 0.4466 time to fit residues: 23.5166 Evaluate side-chains 48 residues out of total 222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 223 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 6 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 20 optimal weight: 0.0970 chunk 7 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 0.0870 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 10 optimal weight: 0.0000 chunk 15 optimal weight: 0.0980 overall best weight: 0.1960 ------------------------------------------------------------------------------- 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: 0.6999 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2014 Z= 0.211 Angle : 0.611 7.155 2767 Z= 0.293 Chirality : 0.042 0.204 348 Planarity : 0.005 0.042 325 Dihedral : 9.285 111.574 306 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.50 % Allowed : 16.00 % Favored : 80.50 % 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: 0.69 (0.52), residues: 248 helix: 0.73 (0.37), residues: 196 sheet: None (None), residues: 0 loop : -0.17 (0.86), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 121 HIS 0.005 0.002 HIS R 145 PHE 0.011 0.001 PHE R 92 TYR 0.008 0.001 TYR R 87 ARG 0.001 0.000 ARG R 153 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: R 332 LEU cc_start: 0.7147 (mt) cc_final: 0.6929 (tp) outliers start: 7 outliers final: 3 residues processed: 52 average time/residue: 0.4146 time to fit residues: 22.6852 Evaluate side-chains 50 residues out of total 222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 331 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 22 optimal weight: 0.2980 chunk 24 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 0.2980 chunk 6 optimal weight: 0.8980 chunk 20 optimal weight: 0.0980 chunk 13 optimal weight: 0.0670 chunk 0 optimal weight: 0.9990 chunk 17 optimal weight: 0.0670 chunk 9 optimal weight: 0.5980 chunk 16 optimal weight: 0.0770 overall best weight: 0.1214 ------------------------------------------------------------------------------- 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: 0.6985 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2014 Z= 0.178 Angle : 0.592 6.482 2767 Z= 0.285 Chirality : 0.041 0.193 348 Planarity : 0.005 0.039 325 Dihedral : 7.744 83.774 306 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 5.00 % Allowed : 17.50 % Favored : 77.50 % 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: 0.86 (0.53), residues: 248 helix: 0.73 (0.36), residues: 198 sheet: None (None), residues: 0 loop : 0.42 (0.96), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 121 HIS 0.005 0.002 HIS R 145 PHE 0.009 0.001 PHE R 217 TYR 0.021 0.001 TYR R 370 ARG 0.001 0.000 ARG R 153 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 43 time to evaluate : 0.206 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 49 average time/residue: 0.4773 time to fit residues: 24.5857 Evaluate side-chains 45 residues out of total 222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 184 ILE Chi-restraints excluded: chain R residue 331 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 0 optimal weight: 0.9990 chunk 12 optimal weight: 0.0000 chunk 21 optimal weight: 0.2980 chunk 6 optimal weight: 0.8980 chunk 8 optimal weight: 0.1980 chunk 4 optimal weight: 0.0670 chunk 14 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 11 optimal weight: 0.2980 overall best weight: 0.1722 ------------------------------------------------------------------------------- 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: 0.7008 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2014 Z= 0.201 Angle : 0.613 6.625 2767 Z= 0.291 Chirality : 0.041 0.197 348 Planarity : 0.005 0.037 325 Dihedral : 6.336 53.781 306 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 4.50 % Allowed : 19.50 % Favored : 76.00 % 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: 0.83 (0.52), residues: 248 helix: 0.73 (0.36), residues: 198 sheet: None (None), residues: 0 loop : 0.30 (0.88), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 121 HIS 0.005 0.002 HIS R 145 PHE 0.010 0.001 PHE R 217 TYR 0.008 0.001 TYR R 370 ARG 0.001 0.000 ARG R 153 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.228 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 48 average time/residue: 0.4475 time to fit residues: 22.6080 Evaluate side-chains 48 residues out of total 222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 40 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 94 MET Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 331 PHE Chi-restraints excluded: chain R residue 335 LEU Chi-restraints excluded: chain R residue 348 VAL Chi-restraints excluded: chain R residue 385 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 2 optimal weight: 0.7980 chunk 8 optimal weight: 0.0050 chunk 12 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 chunk 13 optimal weight: 0.3980 chunk 17 optimal weight: 0.4980 chunk 20 optimal weight: 0.0970 chunk 24 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 11 optimal weight: 0.3980 overall best weight: 0.2792 ------------------------------------------------------------------------------- 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: 0.7066 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 2014 Z= 0.261 Angle : 0.661 6.868 2767 Z= 0.319 Chirality : 0.044 0.220 348 Planarity : 0.005 0.034 325 Dihedral : 5.907 36.198 306 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 5.50 % Allowed : 21.00 % Favored : 73.50 % 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: 0.55 (0.52), residues: 248 helix: 0.47 (0.36), residues: 204 sheet: None (None), residues: 0 loop : 0.50 (0.87), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 121 HIS 0.004 0.002 HIS R 145 PHE 0.011 0.001 PHE R 217 TYR 0.011 0.002 TYR R 370 ARG 0.001 0.000 ARG R 153 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 45 time to evaluate : 0.219 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 51 average time/residue: 0.4677 time to fit residues: 25.0043 Evaluate side-chains 51 residues out of total 222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 94 MET Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 171 THR Chi-restraints excluded: chain R residue 331 PHE Chi-restraints excluded: chain R residue 335 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 14 optimal weight: 0.6980 chunk 9 optimal weight: 0.3980 chunk 7 optimal weight: 0.0970 chunk 4 optimal weight: 0.0770 chunk 15 optimal weight: 0.3980 chunk 16 optimal weight: 0.1980 chunk 11 optimal weight: 0.0870 chunk 2 optimal weight: 0.2980 chunk 18 optimal weight: 0.6980 chunk 21 optimal weight: 0.0570 chunk 23 optimal weight: 0.0030 overall best weight: 0.0642 ------------------------------------------------------------------------------- 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: 0.6963 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2014 Z= 0.168 Angle : 0.631 6.569 2767 Z= 0.298 Chirality : 0.040 0.177 348 Planarity : 0.005 0.035 325 Dihedral : 5.387 42.988 306 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 4.50 % Allowed : 23.50 % Favored : 72.00 % 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: 0.75 (0.52), residues: 248 helix: 0.67 (0.37), residues: 196 sheet: None (None), residues: 0 loop : 0.31 (0.83), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 121 HIS 0.003 0.001 HIS R 145 PHE 0.008 0.001 PHE R 330 TYR 0.022 0.001 TYR R 370 ARG 0.000 0.000 ARG R 153 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 40 time to evaluate : 0.211 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 46 average time/residue: 0.4448 time to fit residues: 21.5087 Evaluate side-chains 44 residues out of total 222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 184 ILE Chi-restraints excluded: chain R residue 331 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 0.5980 chunk 22 optimal weight: 0.0980 chunk 23 optimal weight: 0.4980 chunk 13 optimal weight: 0.0010 chunk 9 optimal weight: 0.4980 chunk 17 optimal weight: 0.0670 chunk 6 optimal weight: 0.5980 chunk 20 optimal weight: 0.4980 chunk 14 optimal weight: 0.5980 chunk 11 optimal weight: 0.3980 chunk 16 optimal weight: 0.0980 overall best weight: 0.1324 ------------------------------------------------------------------------------- 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: 0.6996 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2014 Z= 0.188 Angle : 0.633 7.176 2767 Z= 0.298 Chirality : 0.041 0.187 348 Planarity : 0.004 0.031 325 Dihedral : 5.347 39.845 306 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.00 % Allowed : 25.00 % Favored : 72.00 % 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: 0.77 (0.52), residues: 248 helix: 0.68 (0.36), residues: 198 sheet: None (None), residues: 0 loop : 0.31 (0.83), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 180 HIS 0.003 0.001 HIS R 145 PHE 0.009 0.001 PHE R 330 TYR 0.007 0.001 TYR R 370 ARG 0.001 0.000 ARG R 153 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.210 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 46 average time/residue: 0.4397 time to fit residues: 21.2740 Evaluate side-chains 45 residues out of total 222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 331 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 24 optimal weight: 0.3980 chunk 22 optimal weight: 0.5980 chunk 19 optimal weight: 0.4980 chunk 2 optimal weight: 0.8980 chunk 15 optimal weight: 0.2980 chunk 12 optimal weight: 0.4980 chunk 21 optimal weight: 0.0980 chunk 6 optimal weight: 0.9980 chunk 18 optimal weight: 0.1980 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 0.1980 overall best weight: 0.2380 ------------------------------------------------------------------------------- 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: 0.7044 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 2014 Z= 0.239 Angle : 0.652 7.523 2767 Z= 0.312 Chirality : 0.042 0.199 348 Planarity : 0.004 0.031 325 Dihedral : 5.590 43.269 306 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.00 % Allowed : 25.50 % Favored : 72.50 % 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: 0.55 (0.52), residues: 248 helix: 0.56 (0.36), residues: 198 sheet: None (None), residues: 0 loop : 0.08 (0.79), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 367 HIS 0.003 0.002 HIS R 145 PHE 0.010 0.001 PHE R 330 TYR 0.027 0.002 TYR R 370 ARG 0.002 0.000 ARG R 153 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.218 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 47 average time/residue: 0.4979 time to fit residues: 24.4612 Evaluate side-chains 46 residues out of total 222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 331 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 20 optimal weight: 0.2980 chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 0.0980 chunk 17 optimal weight: 0.4980 chunk 1 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 0.4980 chunk 13 optimal weight: 0.3980 chunk 0 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 0.3980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 72 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 2014 Z= 0.295 Angle : 0.696 7.585 2767 Z= 0.335 Chirality : 0.044 0.210 348 Planarity : 0.005 0.031 325 Dihedral : 5.977 42.607 306 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.00 % Allowed : 25.50 % Favored : 72.50 % 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: 0.14 (0.50), residues: 248 helix: 0.23 (0.35), residues: 202 sheet: None (None), residues: 0 loop : 0.12 (0.81), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP R 131 HIS 0.002 0.001 HIS R 145 PHE 0.013 0.002 PHE R 330 TYR 0.010 0.002 TYR R 87 ARG 0.002 0.000 ARG R 153 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: R 63 MET cc_start: 0.4960 (ttm) cc_final: 0.4130 (tmm) outliers start: 4 outliers final: 4 residues processed: 45 average time/residue: 0.5156 time to fit residues: 24.2739 Evaluate side-chains 46 residues out of total 222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 331 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 9 optimal weight: 0.4980 chunk 24 optimal weight: 0.0570 chunk 0 optimal weight: 0.9990 chunk 4 optimal weight: 0.1980 chunk 3 optimal weight: 0.0980 chunk 5 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 10 optimal weight: 0.0870 chunk 2 optimal weight: 0.4980 chunk 6 optimal weight: 0.0870 overall best weight: 0.1054 ------------------------------------------------------------------------------- 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 = 0.4057 r_free = 0.4057 target = 0.155918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.143370 restraints weight = 2626.330| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 1.58 r_work: 0.3821 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3695 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2014 Z= 0.185 Angle : 0.638 6.907 2767 Z= 0.304 Chirality : 0.040 0.189 348 Planarity : 0.004 0.031 325 Dihedral : 5.698 42.871 306 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.00 % Allowed : 23.50 % Favored : 73.50 % 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: 0.36 (0.51), residues: 248 helix: 0.40 (0.36), residues: 198 sheet: None (None), residues: 0 loop : 0.13 (0.82), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 121 HIS 0.003 0.001 HIS R 145 PHE 0.009 0.001 PHE R 330 TYR 0.008 0.001 TYR R 370 ARG 0.001 0.000 ARG R 153 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1245.31 seconds wall clock time: 22 minutes 40.17 seconds (1360.17 seconds total)