Starting phenix.real_space_refine on Sun Mar 10 20:18:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iy6_35815/03_2024/8iy6_35815.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iy6_35815/03_2024/8iy6_35815.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iy6_35815/03_2024/8iy6_35815.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iy6_35815/03_2024/8iy6_35815.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iy6_35815/03_2024/8iy6_35815.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iy6_35815/03_2024/8iy6_35815.pdb" } resolution = 3.13 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 ------------------------------------------------------------------------------- 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= -0.041 sd= 0.433 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 2297 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 29 5.16 5 C 1650 2.51 5 N 395 2.21 5 O 421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None 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: 2495 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2324 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 293, 2321 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 280} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 293, 2321 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 280} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2371 Chain: "L" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 171 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Time building chain proxies: 2.94, per 1000 atoms: 1.18 Number of scatterers: 2495 At special positions: 0 Unit cell: (66.234, 67.396, 80.178, 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 29 16.00 O 421 8.00 N 395 7.00 C 1650 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 358 " distance=2.03 Simple disulfide: pdb=" SG CYS R 174 " - pdb=" SG CYS R 255 " distance=2.03 Simple disulfide: pdb=" SG CYS L 1 " - pdb=" SG CYS L 15 " distance=2.03 Simple disulfide: pdb=" SG CYS L 3 " - pdb=" SG CYS L 11 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 893.1 milliseconds 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 610 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 1 sheets defined 82.5% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'R' and resid 97 through 129 Processing helix chain 'R' and resid 130 through 133 Processing helix chain 'R' and resid 134 through 165 Proline residue: R 156 - end of helix Processing helix chain 'R' and resid 170 through 205 removed outlier: 3.686A pdb=" N CYS R 174 " --> pdb=" O GLY R 170 " (cutoff:3.500A) Proline residue: R 178 - end of helix Processing helix chain 'R' and resid 219 through 233 Processing helix chain 'R' and resid 233 through 239 Processing helix chain 'R' and resid 263 through 281 removed outlier: 6.312A pdb=" N ASP R 274 " --> pdb=" O LYS R 270 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N TRP R 275 " --> pdb=" O THR R 271 " (cutoff:3.500A) Processing helix chain 'R' and resid 282 through 303 Processing helix chain 'R' and resid 319 through 350 Proline residue: R 338 - end of helix Processing helix chain 'R' and resid 357 through 390 removed outlier: 3.703A pdb=" N VAL R 366 " --> pdb=" O SER R 362 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASN R 382 " --> pdb=" O ASN R 378 " (cutoff:3.500A) Proline residue: R 383 - end of helix Processing helix chain 'R' and resid 390 through 403 removed outlier: 3.584A pdb=" N CYS R 403 " --> pdb=" O SER R 399 " (cutoff:3.500A) Processing helix chain 'L' and resid 8 through 18 Processing sheet with id=AA1, first strand: chain 'R' and resid 240 through 247 202 hydrogen bonds defined for protein. 599 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: 0.65 Time building geometry restraints manager: 1.21 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: 744 1.34 - 1.46: 622 1.46 - 1.58: 1151 1.58 - 1.70: 0 1.70 - 1.82: 37 Bond restraints: 2554 Sorted by residual: bond pdb=" N CYS L 1 " pdb=" CA CYS L 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" CB ASN R 353 " pdb=" CG ASN R 353 " ideal model delta sigma weight residual 1.516 1.534 -0.018 2.50e-02 1.60e+03 5.34e-01 bond pdb=" CA ASN R 353 " pdb=" CB ASN R 353 " ideal model delta sigma weight residual 1.541 1.549 -0.008 1.20e-02 6.94e+03 4.07e-01 bond pdb=" CD LYS R 175 " pdb=" CE LYS R 175 " ideal model delta sigma weight residual 1.520 1.502 0.018 3.00e-02 1.11e+03 3.46e-01 bond pdb=" CG PRO R 136 " pdb=" CD PRO R 136 " ideal model delta sigma weight residual 1.503 1.486 0.017 3.40e-02 8.65e+02 2.41e-01 ... (remaining 2549 not shown) Histogram of bond angle deviations from ideal: 100.70 - 107.36: 86 107.36 - 114.02: 1482 114.02 - 120.68: 1106 120.68 - 127.33: 772 127.33 - 133.99: 28 Bond angle restraints: 3474 Sorted by residual: angle pdb=" N ILE R 238 " pdb=" CA ILE R 238 " pdb=" C ILE R 238 " ideal model delta sigma weight residual 113.47 109.23 4.24 1.01e+00 9.80e-01 1.77e+01 angle pdb=" N ILE R 381 " pdb=" CA ILE R 381 " pdb=" C ILE R 381 " ideal model delta sigma weight residual 110.62 112.83 -2.21 1.02e+00 9.61e-01 4.69e+00 angle pdb=" CA ILE R 238 " pdb=" C ILE R 238 " pdb=" O ILE R 238 " ideal model delta sigma weight residual 118.98 120.65 -1.67 9.00e-01 1.23e+00 3.43e+00 angle pdb=" CA ASN R 353 " pdb=" CB ASN R 353 " pdb=" CG ASN R 353 " ideal model delta sigma weight residual 112.60 114.38 -1.78 1.00e+00 1.00e+00 3.16e+00 angle pdb=" N ASN R 353 " pdb=" CA ASN R 353 " pdb=" CB ASN R 353 " ideal model delta sigma weight residual 114.17 112.18 1.99 1.14e+00 7.69e-01 3.04e+00 ... (remaining 3469 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.65: 1367 15.65 - 31.29: 134 31.29 - 46.93: 25 46.93 - 62.58: 3 62.58 - 78.22: 3 Dihedral angle restraints: 1532 sinusoidal: 597 harmonic: 935 Sorted by residual: dihedral pdb=" CB CYS R 90 " pdb=" SG CYS R 90 " pdb=" SG CYS R 358 " pdb=" CB CYS R 358 " ideal model delta sinusoidal sigma weight residual 93.00 45.46 47.54 1 1.00e+01 1.00e-02 3.12e+01 dihedral pdb=" CA MET R 245 " pdb=" C MET R 245 " pdb=" N ASP R 246 " pdb=" CA ASP R 246 " ideal model delta harmonic sigma weight residual 180.00 156.55 23.45 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" SG CYS L 1 " pdb=" CB CYS L 15 " pdb=" SG CYS L 15 " pdb=" CA CYS L 15 " ideal model delta sinusoidal sigma weight residual 79.00 3.83 75.17 1 2.00e+01 2.50e-03 1.79e+01 ... (remaining 1529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 291 0.030 - 0.061: 80 0.061 - 0.091: 35 0.091 - 0.121: 10 0.121 - 0.152: 2 Chirality restraints: 418 Sorted by residual: chirality pdb=" CA ILE R 254 " pdb=" N ILE R 254 " pdb=" C ILE R 254 " pdb=" CB ILE R 254 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" CA ILE R 94 " pdb=" N ILE R 94 " pdb=" C ILE R 94 " pdb=" CB ILE R 94 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ILE R 96 " pdb=" N ILE R 96 " pdb=" C ILE R 96 " pdb=" CB ILE R 96 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.36e-01 ... (remaining 415 not shown) Planarity restraints: 416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN R 353 " 0.009 2.00e-02 2.50e+03 1.87e-02 3.49e+00 pdb=" C ASN R 353 " -0.032 2.00e-02 2.50e+03 pdb=" O ASN R 353 " 0.012 2.00e-02 2.50e+03 pdb=" N ASP R 354 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY R 92 " -0.029 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO R 93 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO R 93 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO R 93 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 112 " -0.010 2.00e-02 2.50e+03 7.22e-03 9.13e-01 pdb=" CG PHE R 112 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 PHE R 112 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE R 112 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE R 112 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE R 112 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE R 112 " -0.005 2.00e-02 2.50e+03 ... (remaining 413 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 74 2.71 - 3.26: 2685 3.26 - 3.81: 4148 3.81 - 4.35: 4868 4.35 - 4.90: 8375 Nonbonded interactions: 20150 Sorted by model distance: nonbonded pdb=" OG SER R 342 " pdb=" OD1 ASP R 368 " model vdw 2.168 2.440 nonbonded pdb=" O ASN R 353 " pdb=" OD1 ASN R 353 " model vdw 2.231 3.040 nonbonded pdb=" NZ LYS R 161 " pdb=" O ASP L 18 " model vdw 2.293 2.520 nonbonded pdb=" OG SER R 108 " pdb=" OD1 ASN R 373 " model vdw 2.354 2.440 nonbonded pdb=" O ASP R 354 " pdb=" NH1 ARG R 357 " model vdw 2.363 2.520 ... (remaining 20145 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=0.30 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: 0.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.300 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5984 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 : 0.003 0.033 2554 Z= 0.170 Angle : 0.545 4.771 3474 Z= 0.308 Chirality : 0.036 0.152 418 Planarity : 0.004 0.043 416 Dihedral : 12.047 78.223 910 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % 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: 1.84 (0.48), residues: 307 helix: 1.90 (0.33), residues: 242 sheet: -1.52 (1.40), residues: 10 loop : -1.31 (0.79), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 276 HIS 0.003 0.001 HIS R 258 PHE 0.015 0.001 PHE R 112 TYR 0.007 0.001 TYR R 200 ARG 0.003 0.000 ARG R 343 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.257 Fit side-chains REVERT: R 133 ARG cc_start: 0.6820 (tmm-80) cc_final: 0.6597 (ttp-170) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1965 time to fit residues: 13.0233 Evaluate side-chains 46 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 26 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6062 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2554 Z= 0.266 Angle : 0.690 7.850 3474 Z= 0.357 Chirality : 0.045 0.268 418 Planarity : 0.005 0.045 416 Dihedral : 4.681 22.719 337 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.42 % Allowed : 8.51 % Favored : 90.07 % 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: 1.61 (0.48), residues: 307 helix: 1.63 (0.32), residues: 245 sheet: -1.33 (1.40), residues: 10 loop : -1.05 (0.93), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 276 HIS 0.007 0.002 HIS R 258 PHE 0.027 0.003 PHE R 100 TYR 0.010 0.002 TYR R 281 ARG 0.005 0.001 ARG R 343 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.298 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 50 average time/residue: 0.1984 time to fit residues: 11.4556 Evaluate side-chains 47 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 224 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 15 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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: 0.6073 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2554 Z= 0.253 Angle : 0.669 8.595 3474 Z= 0.345 Chirality : 0.044 0.277 418 Planarity : 0.005 0.043 416 Dihedral : 4.728 22.622 337 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.42 % Allowed : 12.06 % Favored : 86.52 % 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: 1.50 (0.48), residues: 307 helix: 1.54 (0.32), residues: 244 sheet: -1.02 (1.34), residues: 10 loop : -1.03 (0.96), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 276 HIS 0.006 0.002 HIS R 258 PHE 0.027 0.003 PHE R 100 TYR 0.008 0.002 TYR R 369 ARG 0.004 0.001 ARG R 343 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.263 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 50 average time/residue: 0.1715 time to fit residues: 10.0150 Evaluate side-chains 46 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 365 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 27 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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: 0.6033 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2554 Z= 0.191 Angle : 0.617 6.888 3474 Z= 0.319 Chirality : 0.042 0.269 418 Planarity : 0.005 0.040 416 Dihedral : 4.606 22.387 337 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.84 % Allowed : 9.93 % Favored : 87.23 % 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: 1.98 (0.49), residues: 307 helix: 1.92 (0.32), residues: 244 sheet: -0.80 (1.34), residues: 10 loop : -1.10 (0.96), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 276 HIS 0.005 0.001 HIS R 258 PHE 0.029 0.002 PHE R 100 TYR 0.009 0.001 TYR R 350 ARG 0.005 0.001 ARG R 253 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 47 time to evaluate : 0.322 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 51 average time/residue: 0.1793 time to fit residues: 10.7512 Evaluate side-chains 52 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 250 SER Chi-restraints excluded: chain R residue 365 LEU Chi-restraints excluded: chain R residue 367 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 17 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 12 optimal weight: 0.2980 chunk 25 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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: 0.5983 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2554 Z= 0.169 Angle : 0.590 6.752 3474 Z= 0.302 Chirality : 0.040 0.262 418 Planarity : 0.004 0.037 416 Dihedral : 4.451 21.388 337 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.84 % Allowed : 10.64 % Favored : 86.52 % 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: 2.32 (0.49), residues: 307 helix: 2.14 (0.33), residues: 244 sheet: -0.77 (1.30), residues: 10 loop : -0.87 (1.00), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 276 HIS 0.003 0.001 HIS R 258 PHE 0.033 0.002 PHE R 100 TYR 0.010 0.001 TYR R 350 ARG 0.007 0.001 ARG R 253 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.293 Fit side-chains REVERT: R 134 ASN cc_start: 0.7715 (p0) cc_final: 0.7358 (p0) REVERT: R 241 ASP cc_start: 0.7326 (OUTLIER) cc_final: 0.6920 (m-30) outliers start: 8 outliers final: 7 residues processed: 48 average time/residue: 0.1733 time to fit residues: 9.7798 Evaluate side-chains 50 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 241 ASP Chi-restraints excluded: chain R residue 250 SER Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 365 LEU Chi-restraints excluded: chain R residue 367 LEU Chi-restraints excluded: chain L residue 6 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 17 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 24 optimal weight: 0.0980 chunk 13 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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: 0.6031 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2554 Z= 0.200 Angle : 0.621 7.199 3474 Z= 0.317 Chirality : 0.042 0.285 418 Planarity : 0.004 0.038 416 Dihedral : 4.475 21.990 337 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.19 % Allowed : 10.28 % Favored : 86.52 % 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: 2.15 (0.49), residues: 307 helix: 2.02 (0.32), residues: 244 sheet: -0.77 (1.34), residues: 10 loop : -0.92 (0.99), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 276 HIS 0.004 0.001 HIS R 258 PHE 0.031 0.002 PHE R 100 TYR 0.008 0.001 TYR R 350 ARG 0.003 0.000 ARG R 343 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 46 time to evaluate : 0.253 Fit side-chains REVERT: R 134 ASN cc_start: 0.7603 (p0) cc_final: 0.7297 (p0) REVERT: R 241 ASP cc_start: 0.7433 (OUTLIER) cc_final: 0.6410 (m-30) outliers start: 9 outliers final: 7 residues processed: 51 average time/residue: 0.1410 time to fit residues: 8.5963 Evaluate side-chains 55 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 47 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 241 ASP Chi-restraints excluded: chain R residue 250 SER Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 365 LEU Chi-restraints excluded: chain R residue 367 LEU Chi-restraints excluded: chain L residue 6 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 18 optimal weight: 0.2980 chunk 13 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- 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: 0.6031 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2554 Z= 0.203 Angle : 0.619 7.253 3474 Z= 0.317 Chirality : 0.042 0.282 418 Planarity : 0.004 0.036 416 Dihedral : 4.555 22.087 337 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.84 % Allowed : 10.28 % Favored : 86.88 % 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: 2.07 (0.49), residues: 307 helix: 1.95 (0.32), residues: 244 sheet: -0.75 (1.31), residues: 10 loop : -0.91 (0.98), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 276 HIS 0.004 0.001 HIS R 258 PHE 0.032 0.002 PHE R 100 TYR 0.017 0.002 TYR R 387 ARG 0.003 0.001 ARG R 343 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.300 Fit side-chains REVERT: R 134 ASN cc_start: 0.7615 (p0) cc_final: 0.7326 (p0) REVERT: R 241 ASP cc_start: 0.7443 (OUTLIER) cc_final: 0.6218 (m-30) outliers start: 8 outliers final: 7 residues processed: 50 average time/residue: 0.1707 time to fit residues: 10.1266 Evaluate side-chains 53 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 241 ASP Chi-restraints excluded: chain R residue 250 SER Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 365 LEU Chi-restraints excluded: chain R residue 367 LEU Chi-restraints excluded: chain L residue 6 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 2 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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: 0.6007 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2554 Z= 0.182 Angle : 0.606 7.164 3474 Z= 0.310 Chirality : 0.041 0.280 418 Planarity : 0.004 0.035 416 Dihedral : 4.498 22.202 337 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.19 % Allowed : 10.64 % Favored : 86.17 % 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: 2.28 (0.49), residues: 307 helix: 2.09 (0.33), residues: 244 sheet: -0.57 (1.35), residues: 10 loop : -0.80 (0.98), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 276 HIS 0.004 0.001 HIS R 258 PHE 0.033 0.002 PHE R 100 TYR 0.010 0.001 TYR R 350 ARG 0.003 0.001 ARG R 253 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.245 Fit side-chains REVERT: R 134 ASN cc_start: 0.7524 (p0) cc_final: 0.7282 (p0) REVERT: R 241 ASP cc_start: 0.7427 (OUTLIER) cc_final: 0.6184 (m-30) outliers start: 9 outliers final: 7 residues processed: 50 average time/residue: 0.1672 time to fit residues: 9.8281 Evaluate side-chains 53 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 241 ASP Chi-restraints excluded: chain R residue 250 SER Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 365 LEU Chi-restraints excluded: chain R residue 366 VAL Chi-restraints excluded: chain R residue 367 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 29 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 13 optimal weight: 0.0770 chunk 20 optimal weight: 0.1980 chunk 30 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5934 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2554 Z= 0.152 Angle : 0.596 7.477 3474 Z= 0.302 Chirality : 0.040 0.274 418 Planarity : 0.004 0.033 416 Dihedral : 4.325 20.654 337 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.84 % Allowed : 10.99 % Favored : 86.17 % 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: 2.64 (0.49), residues: 307 helix: 2.34 (0.33), residues: 244 sheet: -0.43 (1.38), residues: 10 loop : -0.69 (0.99), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 276 HIS 0.004 0.001 HIS R 258 PHE 0.033 0.002 PHE R 100 TYR 0.011 0.001 TYR R 350 ARG 0.005 0.001 ARG R 253 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.301 Fit side-chains REVERT: R 241 ASP cc_start: 0.7223 (OUTLIER) cc_final: 0.6072 (m-30) REVERT: R 296 MET cc_start: 0.7138 (ttp) cc_final: 0.6902 (ttm) outliers start: 8 outliers final: 5 residues processed: 52 average time/residue: 0.1759 time to fit residues: 10.7873 Evaluate side-chains 50 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 241 ASP Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 365 LEU Chi-restraints excluded: chain R residue 366 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 26 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 6 optimal weight: 0.4980 chunk 24 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 4 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5917 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2554 Z= 0.154 Angle : 0.593 7.573 3474 Z= 0.301 Chirality : 0.040 0.276 418 Planarity : 0.004 0.030 416 Dihedral : 4.261 20.180 337 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.13 % Allowed : 12.41 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.49), residues: 307 helix: 2.38 (0.33), residues: 245 sheet: -0.50 (1.38), residues: 10 loop : -0.70 (0.99), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 276 HIS 0.005 0.001 HIS R 258 PHE 0.032 0.002 PHE R 100 TYR 0.009 0.001 TYR R 350 ARG 0.003 0.000 ARG R 253 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.290 Fit side-chains REVERT: R 241 ASP cc_start: 0.7183 (OUTLIER) cc_final: 0.6067 (m-30) REVERT: R 296 MET cc_start: 0.7195 (ttp) cc_final: 0.6960 (ttm) outliers start: 6 outliers final: 4 residues processed: 51 average time/residue: 0.1794 time to fit residues: 10.7015 Evaluate side-chains 50 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 241 ASP Chi-restraints excluded: chain R residue 365 LEU Chi-restraints excluded: chain R residue 366 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 17 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.4345 r_free = 0.4345 target = 0.224110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.205514 restraints weight = 8868.417| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 3.25 r_work: 0.4045 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4103 r_free = 0.4103 target_work(ls_wunit_k1) = 0.200 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4102 r_free = 0.4102 target_work(ls_wunit_k1) = 0.200 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4102 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6195 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2554 Z= 0.202 Angle : 0.628 7.378 3474 Z= 0.320 Chirality : 0.042 0.287 418 Planarity : 0.004 0.030 416 Dihedral : 4.386 22.162 337 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.84 % Allowed : 11.70 % Favored : 85.46 % 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: 2.38 (0.49), residues: 307 helix: 2.16 (0.33), residues: 244 sheet: -0.65 (1.34), residues: 10 loop : -0.76 (0.99), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 276 HIS 0.004 0.001 HIS R 258 PHE 0.029 0.002 PHE R 100 TYR 0.008 0.001 TYR R 350 ARG 0.003 0.001 ARG R 343 =============================================================================== Job complete usr+sys time: 852.06 seconds wall clock time: 16 minutes 4.73 seconds (964.73 seconds total)