Starting phenix.real_space_refine on Thu Dec 7 21:11:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iy6_35815/12_2023/8iy6_35815.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iy6_35815/12_2023/8iy6_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_35815/12_2023/8iy6_35815.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iy6_35815/12_2023/8iy6_35815.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iy6_35815/12_2023/8iy6_35815.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iy6_35815/12_2023/8iy6_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-1.21rc1-5172/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: 3.17, per 1000 atoms: 1.27 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: 1.08 Conformation dependent library (CDL) restraints added in 860.9 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: 0.25 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: 0.66 Time building geometry restraints manager: 1.18 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: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.070 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.320 ------------------------------------------------------------------------------- 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 : 0.248 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1934 time to fit residues: 12.7848 Evaluate side-chains 45 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.276 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3952 ------------------------------------------------------------------------------- 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: 0.6060 moved from start: 0.1252 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= 0.263 Angle : 0.690 7.815 3474 Z= 0.357 Chirality : 0.044 0.264 418 Planarity : 0.005 0.044 416 Dihedral : 4.675 22.589 337 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.87 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: 1.62 (0.48), residues: 307 helix: 1.64 (0.32), residues: 245 sheet: -1.34 (1.39), residues: 10 loop : -1.03 (0.92), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 276 HIS 0.006 0.002 HIS R 258 PHE 0.027 0.003 PHE R 100 TYR 0.011 0.002 TYR R 350 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 51 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.272 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 49 average time/residue: 0.1714 time to fit residues: 9.8174 Evaluate side-chains 45 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 0.289 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0288 time to fit residues: 0.5202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 23 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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: 0.6054 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2554 Z= 0.235 Angle : 0.659 8.719 3474 Z= 0.338 Chirality : 0.043 0.270 418 Planarity : 0.005 0.042 416 Dihedral : 4.666 22.337 337 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.71 % Allowed : 12.77 % 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: 1.65 (0.48), residues: 307 helix: 1.66 (0.32), residues: 244 sheet: -0.99 (1.36), residues: 10 loop : -1.04 (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 0.028 0.002 PHE R 100 TYR 0.009 0.001 TYR R 281 ARG 0.005 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 51 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.284 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 50 average time/residue: 0.1759 time to fit residues: 10.3629 Evaluate side-chains 47 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 0.307 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0294 time to fit residues: 0.4768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 14 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 29 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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: 0.6052 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2554 Z= 0.217 Angle : 0.627 7.228 3474 Z= 0.325 Chirality : 0.040 0.133 418 Planarity : 0.005 0.042 416 Dihedral : 4.658 22.381 337 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.42 % Allowed : 10.99 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.48), residues: 307 helix: 1.80 (0.32), residues: 244 sheet: -0.85 (1.34), residues: 10 loop : -1.17 (0.94), 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 0.003 PHE R 100 TYR 0.009 0.001 TYR R 350 ARG 0.003 0.001 ARG R 343 *********************** 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 51 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.289 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 48 average time/residue: 0.1715 time to fit residues: 9.6795 Evaluate side-chains 48 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.267 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0297 time to fit residues: 0.5416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 12 optimal weight: 0.0970 chunk 25 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 20.0000 chunk 26 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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: 0.6036 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2554 Z= 0.193 Angle : 0.627 9.047 3474 Z= 0.319 Chirality : 0.043 0.306 418 Planarity : 0.005 0.038 416 Dihedral : 4.575 22.692 337 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.42 % Allowed : 11.70 % 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: 2.01 (0.49), residues: 307 helix: 1.93 (0.33), residues: 244 sheet: -0.51 (1.35), residues: 10 loop : -1.07 (0.97), 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 0.031 0.002 PHE R 100 TYR 0.008 0.001 TYR R 281 ARG 0.003 0.001 ARG R 343 *********************** 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 52 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.280 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 51 average time/residue: 0.1699 time to fit residues: 10.2111 Evaluate side-chains 48 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.288 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0277 time to fit residues: 0.4917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 17 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 29 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 13 optimal weight: 0.5980 chunk 2 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- 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: 0.6041 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2554 Z= 0.194 Angle : 0.627 9.832 3474 Z= 0.318 Chirality : 0.043 0.334 418 Planarity : 0.004 0.038 416 Dihedral : 4.530 22.610 337 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.77 % Allowed : 11.70 % 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: 2.01 (0.49), residues: 307 helix: 1.93 (0.32), residues: 244 sheet: -0.49 (1.33), residues: 10 loop : -1.12 (0.96), 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 0.009 0.001 TYR R 350 ARG 0.003 0.001 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 51 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.282 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 48 average time/residue: 0.1544 time to fit residues: 8.8798 Evaluate side-chains 47 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.280 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0292 time to fit residues: 0.5635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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: 0.6094 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 2554 Z= 0.279 Angle : 0.697 9.562 3474 Z= 0.354 Chirality : 0.046 0.364 418 Planarity : 0.005 0.040 416 Dihedral : 4.743 23.463 337 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.35 % Allowed : 11.70 % Favored : 87.94 % 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: 1.53 (0.48), residues: 307 helix: 1.58 (0.32), residues: 244 sheet: -0.53 (1.29), residues: 10 loop : -1.21 (0.96), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 276 HIS 0.006 0.001 HIS R 258 PHE 0.030 0.003 PHE R 100 TYR 0.008 0.002 TYR R 200 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 48 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.305 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 48 average time/residue: 0.1840 time to fit residues: 10.2607 Evaluate side-chains 47 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.281 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 2 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2554 Z= 0.187 Angle : 0.623 8.967 3474 Z= 0.317 Chirality : 0.042 0.312 418 Planarity : 0.004 0.036 416 Dihedral : 4.609 23.314 337 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.71 % Allowed : 12.06 % 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: 1.94 (0.49), residues: 307 helix: 1.87 (0.33), residues: 244 sheet: -0.26 (1.31), residues: 10 loop : -1.11 (0.96), 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 0.034 0.002 PHE R 100 TYR 0.012 0.001 TYR R 350 ARG 0.003 0.000 ARG R 343 *********************** 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 48 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.267 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 47 average time/residue: 0.1689 time to fit residues: 9.3390 Evaluate side-chains 46 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.254 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0274 time to fit residues: 0.4096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 29 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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: 0.6032 moved from start: 0.2106 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= 0.189 Angle : 0.635 8.906 3474 Z= 0.321 Chirality : 0.042 0.315 418 Planarity : 0.004 0.036 416 Dihedral : 4.575 22.894 337 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.42 % Allowed : 11.70 % 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: 2.04 (0.49), residues: 307 helix: 1.93 (0.32), residues: 244 sheet: -0.14 (1.35), residues: 10 loop : -1.03 (0.97), 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 0.032 0.002 PHE R 100 TYR 0.010 0.001 TYR R 350 ARG 0.004 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 49 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.290 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 47 average time/residue: 0.1801 time to fit residues: 9.9623 Evaluate side-chains 45 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 0.282 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0290 time to fit residues: 0.4932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 26 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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: 0.6068 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 2554 Z= 0.231 Angle : 0.668 9.147 3474 Z= 0.339 Chirality : 0.044 0.345 418 Planarity : 0.005 0.037 416 Dihedral : 4.692 25.706 337 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.71 % Allowed : 12.41 % 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: 1.82 (0.48), residues: 307 helix: 1.78 (0.32), residues: 244 sheet: -0.37 (1.37), residues: 10 loop : -1.10 (0.98), 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 0.030 0.002 PHE R 100 TYR 0.010 0.001 TYR R 350 ARG 0.004 0.001 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 51 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.263 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 50 average time/residue: 0.1727 time to fit residues: 10.1006 Evaluate side-chains 49 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.248 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0299 time to fit residues: 0.4564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 17 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.4331 r_free = 0.4331 target = 0.222874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.203931 restraints weight = 8763.137| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 3.27 r_work: 0.4028 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4010 r_free = 0.4010 target_work(ls_wunit_k1) = 0.192 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4010 r_free = 0.4010 target_work(ls_wunit_k1) = 0.192 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6230 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 2554 Z= 0.224 Angle : 0.683 8.721 3474 Z= 0.350 Chirality : 0.043 0.295 418 Planarity : 0.005 0.036 416 Dihedral : 4.724 26.223 337 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.71 % Allowed : 12.77 % 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: 1.86 (0.48), residues: 307 helix: 1.80 (0.33), residues: 244 sheet: -0.23 (1.31), residues: 10 loop : -1.10 (0.95), 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 0.034 0.002 PHE R 100 TYR 0.010 0.001 TYR R 350 ARG 0.006 0.001 ARG R 357 =============================================================================== Job complete usr+sys time: 856.35 seconds wall clock time: 16 minutes 4.67 seconds (964.67 seconds total)