Starting phenix.real_space_refine on Thu Dec 7 15:51:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpk_26058/12_2023/7tpk_26058.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpk_26058/12_2023/7tpk_26058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpk_26058/12_2023/7tpk_26058.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpk_26058/12_2023/7tpk_26058.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpk_26058/12_2023/7tpk_26058.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpk_26058/12_2023/7tpk_26058.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 8 5.16 5 C 966 2.51 5 N 247 2.21 5 O 263 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 1484 Number of models: 1 Model: "" Number of chains: 1 Chain: "E" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1484 Unusual residues: {'NAG': 1} Classifications: {'peptide': 194, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 10, 'TRANS': 183, None: 1} Not linked: pdbres="GLY E 526 " pdbres="NAG E 601 " Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 7, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 46 Time building chain proxies: 1.43, per 1000 atoms: 0.96 Number of scatterers: 1484 At special positions: 0 Unit cell: (51, 71, 63, 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 8 16.00 O 263 8.00 N 247 7.00 C 966 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.05 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.11 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.09 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG E 601 " - " ASN E 343 " Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 279.9 milliseconds 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 358 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 4 sheets defined 17.5% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.906A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 386 through 389 Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.736A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing sheet with id=AA1, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.504A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.629A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'E' and resid 473 through 474 44 hydrogen bonds defined for protein. 105 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: 0.36 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 425 1.34 - 1.47: 475 1.47 - 1.60: 620 1.60 - 1.73: 0 1.73 - 1.86: 8 Bond restraints: 1528 Sorted by residual: bond pdb=" NE ARG E 403 " pdb=" CZ ARG E 403 " ideal model delta sigma weight residual 1.326 1.359 -0.033 1.10e-02 8.26e+03 8.93e+00 bond pdb=" NE ARG E 509 " pdb=" CZ ARG E 509 " ideal model delta sigma weight residual 1.326 1.356 -0.030 1.10e-02 8.26e+03 7.45e+00 bond pdb=" NE ARG E 346 " pdb=" CZ ARG E 346 " ideal model delta sigma weight residual 1.326 1.352 -0.026 1.10e-02 8.26e+03 5.45e+00 bond pdb=" CD GLU E 471 " pdb=" OE2 GLU E 471 " ideal model delta sigma weight residual 1.249 1.206 0.043 1.90e-02 2.77e+03 5.18e+00 bond pdb=" CA ASN E 422 " pdb=" CB ASN E 422 " ideal model delta sigma weight residual 1.537 1.498 0.040 1.76e-02 3.23e+03 5.06e+00 ... (remaining 1523 not shown) Histogram of bond angle deviations from ideal: 101.57 - 108.07: 69 108.07 - 114.56: 764 114.56 - 121.06: 791 121.06 - 127.55: 452 127.55 - 134.05: 8 Bond angle restraints: 2084 Sorted by residual: angle pdb=" C LEU E 425 " pdb=" N PRO E 426 " pdb=" CA PRO E 426 " ideal model delta sigma weight residual 120.03 126.94 -6.91 9.90e-01 1.02e+00 4.88e+01 angle pdb=" C SER E 383 " pdb=" N PRO E 384 " pdb=" CA PRO E 384 " ideal model delta sigma weight residual 119.56 126.59 -7.03 1.02e+00 9.61e-01 4.74e+01 angle pdb=" C GLN E 506 " pdb=" N PRO E 507 " pdb=" CA PRO E 507 " ideal model delta sigma weight residual 119.83 126.64 -6.81 1.08e+00 8.57e-01 3.97e+01 angle pdb=" C PHE E 490 " pdb=" N PRO E 491 " pdb=" CA PRO E 491 " ideal model delta sigma weight residual 119.56 125.64 -6.08 1.02e+00 9.61e-01 3.55e+01 angle pdb=" C ALA E 411 " pdb=" N PRO E 412 " pdb=" CA PRO E 412 " ideal model delta sigma weight residual 119.85 125.61 -5.76 1.01e+00 9.80e-01 3.25e+01 ... (remaining 2079 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 14.18: 847 14.18 - 28.36: 41 28.36 - 42.54: 6 42.54 - 56.72: 4 56.72 - 70.89: 2 Dihedral angle restraints: 900 sinusoidal: 334 harmonic: 566 Sorted by residual: dihedral pdb=" CB CYS E 480 " pdb=" SG CYS E 480 " pdb=" SG CYS E 488 " pdb=" CB CYS E 488 " ideal model delta sinusoidal sigma weight residual 93.00 140.69 -47.69 1 1.00e+01 1.00e-02 3.14e+01 dihedral pdb=" N ASN E 501 " pdb=" C ASN E 501 " pdb=" CA ASN E 501 " pdb=" CB ASN E 501 " ideal model delta harmonic sigma weight residual 122.80 134.30 -11.50 0 2.50e+00 1.60e-01 2.12e+01 dihedral pdb=" C ASN E 501 " pdb=" N ASN E 501 " pdb=" CA ASN E 501 " pdb=" CB ASN E 501 " ideal model delta harmonic sigma weight residual -122.60 -132.07 9.47 0 2.50e+00 1.60e-01 1.43e+01 ... (remaining 897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 154 0.079 - 0.157: 59 0.157 - 0.236: 7 0.236 - 0.314: 1 0.314 - 0.393: 2 Chirality restraints: 223 Sorted by residual: chirality pdb=" CA ASN E 501 " pdb=" N ASN E 501 " pdb=" C ASN E 501 " pdb=" CB ASN E 501 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" C1 NAG E 601 " pdb=" ND2 ASN E 343 " pdb=" C2 NAG E 601 " pdb=" O5 NAG E 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CA PHE E 497 " pdb=" N PHE E 497 " pdb=" C PHE E 497 " pdb=" CB PHE E 497 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.32e+00 ... (remaining 220 not shown) Planarity restraints: 270 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 495 " -0.062 2.00e-02 2.50e+03 3.46e-02 2.40e+01 pdb=" CG TYR E 495 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR E 495 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR E 495 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR E 495 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR E 495 " 0.021 2.00e-02 2.50e+03 pdb=" CZ TYR E 495 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR E 495 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 343 " 0.034 2.00e-02 2.50e+03 3.47e-02 1.50e+01 pdb=" CG ASN E 343 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN E 343 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN E 343 " -0.052 2.00e-02 2.50e+03 pdb=" C1 NAG E 601 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 497 " 0.019 2.00e-02 2.50e+03 1.22e-02 2.60e+00 pdb=" CG PHE E 497 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE E 497 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE E 497 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE E 497 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE E 497 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE E 497 " 0.012 2.00e-02 2.50e+03 ... (remaining 267 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 766 3.00 - 3.48: 1263 3.48 - 3.95: 2399 3.95 - 4.43: 2662 4.43 - 4.90: 4278 Nonbonded interactions: 11368 Sorted by model distance: nonbonded pdb=" O PHE E 497 " pdb=" C GLN E 498 " model vdw 2.528 3.270 nonbonded pdb=" N ASN E 440 " pdb=" N LEU E 441 " model vdw 2.602 2.560 nonbonded pdb=" N LYS E 462 " pdb=" O LYS E 462 " model vdw 2.608 2.496 nonbonded pdb=" N ASP E 389 " pdb=" N LEU E 390 " model vdw 2.626 2.560 nonbonded pdb=" N ALA E 411 " pdb=" O ALA E 411 " model vdw 2.627 2.496 ... (remaining 11363 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 27.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.920 Find NCS groups from input model: 0.040 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 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 : 0.011 0.060 1528 Z= 0.711 Angle : 1.403 7.313 2084 Z= 0.955 Chirality : 0.084 0.393 223 Planarity : 0.006 0.035 269 Dihedral : 9.829 70.895 530 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.56 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.57), residues: 192 helix: -4.18 (0.54), residues: 25 sheet: 1.35 (0.79), residues: 38 loop : -0.52 (0.52), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.006 TRP E 353 PHE 0.019 0.003 PHE E 497 TYR 0.062 0.004 TYR E 495 ARG 0.002 0.000 ARG E 403 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.149 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1892 time to fit residues: 6.9259 Evaluate side-chains 19 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.161 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 16 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 5 optimal weight: 0.0070 chunk 11 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 1528 Z= 0.322 Angle : 0.613 6.724 2084 Z= 0.326 Chirality : 0.047 0.131 223 Planarity : 0.004 0.029 269 Dihedral : 6.098 41.359 238 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.44 % Allowed : 6.47 % Favored : 92.09 % 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 (0.54), residues: 192 helix: -3.88 (0.59), residues: 31 sheet: 0.66 (0.72), residues: 49 loop : -1.31 (0.51), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 436 PHE 0.012 0.002 PHE E 429 TYR 0.013 0.002 TYR E 351 ARG 0.005 0.001 ARG E 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 27 time to evaluate : 0.164 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 29 average time/residue: 0.1549 time to fit residues: 5.1177 Evaluate side-chains 21 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.163 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0220 time to fit residues: 0.2532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 17 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 8 optimal weight: 0.1980 chunk 1 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 9 optimal weight: 0.3980 chunk 16 optimal weight: 0.0980 chunk 4 optimal weight: 0.9980 chunk 15 optimal weight: 0.0980 chunk 10 optimal weight: 0.4980 overall best weight: 0.2580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1528 Z= 0.186 Angle : 0.494 5.840 2084 Z= 0.259 Chirality : 0.044 0.124 223 Planarity : 0.004 0.029 269 Dihedral : 4.899 32.073 238 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.72 % Allowed : 10.79 % Favored : 88.49 % 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: -1.51 (0.54), residues: 192 helix: -3.61 (0.58), residues: 31 sheet: 1.59 (0.87), residues: 37 loop : -1.17 (0.48), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 436 PHE 0.007 0.001 PHE E 497 TYR 0.008 0.001 TYR E 351 ARG 0.004 0.001 ARG E 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 19 time to evaluate : 0.163 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 0.1809 time to fit residues: 3.9531 Evaluate side-chains 18 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.166 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0192 time to fit residues: 0.2558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 0 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 0.0970 chunk 15 optimal weight: 0.0370 chunk 12 optimal weight: 0.0030 chunk 9 optimal weight: 0.6980 chunk 16 optimal weight: 0.0980 chunk 4 optimal weight: 0.3980 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 0.0980 chunk 10 optimal weight: 0.0970 overall best weight: 0.0664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.017 1528 Z= 0.094 Angle : 0.424 4.991 2084 Z= 0.222 Chirality : 0.042 0.127 223 Planarity : 0.003 0.027 269 Dihedral : 4.271 28.801 238 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 10.79 % Favored : 89.21 % 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: -1.25 (0.54), residues: 192 helix: -3.18 (0.74), residues: 25 sheet: 1.86 (0.88), residues: 37 loop : -1.23 (0.46), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 436 PHE 0.007 0.001 PHE E 486 TYR 0.006 0.001 TYR E 473 ARG 0.003 0.000 ARG E 457 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.167 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.2175 time to fit residues: 4.1793 Evaluate side-chains 16 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.160 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 4 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 8 optimal weight: 0.4980 chunk 1 optimal weight: 0.9980 chunk 6 optimal weight: 0.2980 chunk 9 optimal weight: 0.0570 chunk 17 optimal weight: 0.5980 chunk 2 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.3898 ------------------------------------------------------------------------------- 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: 0.7622 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 1528 Z= 0.253 Angle : 0.484 4.191 2084 Z= 0.256 Chirality : 0.044 0.127 223 Planarity : 0.004 0.027 269 Dihedral : 4.858 31.254 238 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.72 % Allowed : 12.23 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.54), residues: 192 helix: -2.96 (0.70), residues: 32 sheet: 1.86 (0.91), residues: 37 loop : -1.32 (0.46), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 436 PHE 0.008 0.001 PHE E 429 TYR 0.009 0.001 TYR E 473 ARG 0.002 0.000 ARG E 346 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.340 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 23 average time/residue: 0.1569 time to fit residues: 4.4588 Evaluate side-chains 22 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 21 time to evaluate : 0.350 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0396 time to fit residues: 0.5798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 10 optimal weight: 0.2980 chunk 15 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 7 optimal weight: 0.2980 chunk 5 optimal weight: 0.0670 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 chunk 1 optimal weight: 0.8980 overall best weight: 0.3518 ------------------------------------------------------------------------------- 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: 0.7636 moved from start: 0.4972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1528 Z= 0.224 Angle : 0.467 3.555 2084 Z= 0.248 Chirality : 0.044 0.130 223 Planarity : 0.004 0.028 269 Dihedral : 4.913 31.845 238 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 13.67 % Favored : 86.33 % 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: -1.41 (0.54), residues: 192 helix: -2.70 (0.75), residues: 32 sheet: 1.63 (0.88), residues: 37 loop : -1.33 (0.45), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 436 PHE 0.008 0.001 PHE E 429 TYR 0.008 0.001 TYR E 473 ARG 0.002 0.000 ARG E 457 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.171 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1814 time to fit residues: 4.5555 Evaluate side-chains 21 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.180 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 14 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 chunk 7 optimal weight: 0.4980 chunk 13 optimal weight: 0.0980 chunk 5 optimal weight: 0.0670 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 0.0980 chunk 18 optimal weight: 0.8980 chunk 8 optimal weight: 0.0060 overall best weight: 0.1534 ------------------------------------------------------------------------------- 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: 0.7589 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1528 Z= 0.123 Angle : 0.426 3.262 2084 Z= 0.225 Chirality : 0.043 0.123 223 Planarity : 0.004 0.027 269 Dihedral : 4.471 29.735 238 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 12.95 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.54), residues: 192 helix: -2.49 (0.79), residues: 32 sheet: 1.68 (0.88), residues: 37 loop : -1.25 (0.45), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 436 PHE 0.005 0.001 PHE E 377 TYR 0.007 0.001 TYR E 473 ARG 0.002 0.000 ARG E 457 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.146 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1945 time to fit residues: 4.8176 Evaluate side-chains 22 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.150 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 0.0270 chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 1 optimal weight: 0.2980 chunk 11 optimal weight: 0.9980 chunk 9 optimal weight: 0.1980 chunk 16 optimal weight: 0.5980 chunk 4 optimal weight: 0.0980 chunk 13 optimal weight: 0.4980 chunk 2 optimal weight: 0.6980 overall best weight: 0.2238 ------------------------------------------------------------------------------- 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: 0.7608 moved from start: 0.5141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 1528 Z= 0.158 Angle : 0.433 3.480 2084 Z= 0.228 Chirality : 0.043 0.127 223 Planarity : 0.003 0.028 269 Dihedral : 4.533 30.210 238 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.72 % Allowed : 13.67 % Favored : 85.61 % 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: -1.38 (0.53), residues: 192 helix: -2.40 (0.80), residues: 32 sheet: 1.51 (0.86), residues: 37 loop : -1.34 (0.45), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 436 PHE 0.006 0.001 PHE E 377 TYR 0.007 0.001 TYR E 473 ARG 0.001 0.000 ARG E 457 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.131 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 22 average time/residue: 0.1948 time to fit residues: 4.8662 Evaluate side-chains 23 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.170 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0194 time to fit residues: 0.2641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 4 optimal weight: 0.0970 chunk 15 optimal weight: 0.0970 chunk 6 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 chunk 2 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 0 optimal weight: 0.3980 chunk 10 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 12 optimal weight: 0.0980 chunk 11 optimal weight: 0.3980 overall best weight: 0.2176 ------------------------------------------------------------------------------- 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: 0.7606 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 1528 Z= 0.153 Angle : 0.430 3.371 2084 Z= 0.226 Chirality : 0.043 0.127 223 Planarity : 0.003 0.028 269 Dihedral : 4.498 29.851 238 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 13.67 % Favored : 86.33 % 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: -1.39 (0.53), residues: 192 helix: -2.28 (0.80), residues: 32 sheet: 1.49 (0.87), residues: 37 loop : -1.38 (0.45), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 436 PHE 0.006 0.001 PHE E 377 TYR 0.007 0.001 TYR E 473 ARG 0.002 0.000 ARG E 457 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.164 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1737 time to fit residues: 4.3837 Evaluate side-chains 22 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.169 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 10 optimal weight: 0.3980 chunk 7 optimal weight: 0.4980 chunk 18 optimal weight: 0.4980 chunk 0 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 15 optimal weight: 0.0670 chunk 17 optimal weight: 0.0980 chunk 8 optimal weight: 0.0980 chunk 1 optimal weight: 0.2980 overall best weight: 0.1918 ------------------------------------------------------------------------------- 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: 0.7599 moved from start: 0.5273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1528 Z= 0.141 Angle : 0.424 3.288 2084 Z= 0.222 Chirality : 0.043 0.125 223 Planarity : 0.003 0.028 269 Dihedral : 4.372 29.115 238 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 14.39 % Favored : 85.61 % 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: -1.34 (0.54), residues: 192 helix: -2.22 (0.82), residues: 32 sheet: 1.56 (0.87), residues: 37 loop : -1.37 (0.45), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 436 PHE 0.005 0.001 PHE E 377 TYR 0.006 0.001 TYR E 351 ARG 0.002 0.000 ARG E 457 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.171 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1934 time to fit residues: 4.8285 Evaluate side-chains 22 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.162 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 4 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 9 optimal weight: 0.4980 chunk 0 optimal weight: 0.9990 chunk 1 optimal weight: 0.1980 chunk 18 optimal weight: 0.2980 chunk 13 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3626 r_free = 0.3626 target = 0.148050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.136247 restraints weight = 2125.719| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.54 r_work: 0.3402 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.5327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 1528 Z= 0.279 Angle : 0.491 4.788 2084 Z= 0.256 Chirality : 0.045 0.133 223 Planarity : 0.004 0.027 269 Dihedral : 5.007 32.852 238 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 15.11 % Favored : 84.89 % 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: -1.51 (0.53), residues: 192 helix: -2.17 (0.85), residues: 32 sheet: 1.46 (0.87), residues: 37 loop : -1.55 (0.44), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 436 PHE 0.010 0.001 PHE E 429 TYR 0.008 0.001 TYR E 351 ARG 0.002 0.000 ARG E 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1295.99 seconds wall clock time: 28 minutes 18.88 seconds (1698.88 seconds total)