Starting phenix.real_space_refine on Sun Mar 10 14:18:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpk_26058/03_2024/7tpk_26058.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpk_26058/03_2024/7tpk_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_26058/03_2024/7tpk_26058.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpk_26058/03_2024/7tpk_26058.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpk_26058/03_2024/7tpk_26058.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpk_26058/03_2024/7tpk_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-dev-5265/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: 1.50, per 1000 atoms: 1.01 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: 0.62 Conformation dependent library (CDL) restraints added in 303.2 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: 0.34 Time building geometry restraints manager: 0.66 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: 5.330 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: 27.040 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.960 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.310 ------------------------------------------------------------------------------- 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 : 0.172 Fit side-chains REVERT: E 438 SER cc_start: 0.7257 (t) cc_final: 0.7019 (t) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1954 time to fit residues: 7.1281 Evaluate side-chains 20 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.164 ------------------------------------------------------------------------------- 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: 0.8980 chunk 18 optimal weight: 0.2980 chunk 15 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 overall best weight: 0.4198 ------------------------------------------------------------------------------- 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: 0.7522 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 1528 Z= 0.295 Angle : 0.597 6.503 2084 Z= 0.317 Chirality : 0.046 0.132 223 Planarity : 0.004 0.028 269 Dihedral : 5.961 41.115 238 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.72 % Allowed : 7.19 % 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: -1.82 (0.54), residues: 192 helix: -3.94 (0.55), residues: 31 sheet: 0.65 (0.71), residues: 49 loop : -1.26 (0.51), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 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 25 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.153 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 25 average time/residue: 0.1692 time to fit residues: 4.8127 Evaluate side-chains 18 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 434 ILE 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: 0.0980 chunk 1 optimal weight: 0.6980 chunk 11 optimal weight: 0.1980 chunk 18 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 16 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 15 optimal weight: 0.0970 chunk 10 optimal weight: 0.4980 overall best weight: 0.2778 ------------------------------------------------------------------------------- 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: 0.7562 moved from start: 0.4103 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= 0.193 Angle : 0.487 4.251 2084 Z= 0.259 Chirality : 0.043 0.120 223 Planarity : 0.004 0.029 269 Dihedral : 4.847 31.369 238 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.72 % Allowed : 11.51 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.54), residues: 192 helix: -3.52 (0.54), residues: 32 sheet: 1.66 (0.88), residues: 37 loop : -1.18 (0.48), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 436 PHE 0.008 0.001 PHE E 497 TYR 0.009 0.001 TYR E 351 ARG 0.003 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 21 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.166 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 20 average time/residue: 0.1756 time to fit residues: 4.0355 Evaluate side-chains 19 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 18 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 367 VAL 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: 0.3980 chunk 7 optimal weight: 0.3980 chunk 15 optimal weight: 0.0870 chunk 12 optimal weight: 0.3980 chunk 9 optimal weight: 0.6980 chunk 16 optimal weight: 0.2980 chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 0.0870 chunk 10 optimal weight: 0.5980 overall best weight: 0.2536 ------------------------------------------------------------------------------- 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: 0.7586 moved from start: 0.4546 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= 0.181 Angle : 0.460 3.893 2084 Z= 0.244 Chirality : 0.043 0.124 223 Planarity : 0.003 0.026 269 Dihedral : 4.719 30.264 238 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.44 % Allowed : 10.79 % Favored : 87.77 % 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 (0.54), residues: 192 helix: -3.15 (0.61), residues: 32 sheet: 1.83 (0.88), residues: 37 loop : -1.23 (0.46), 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 486 TYR 0.007 0.001 TYR E 351 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 22 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 20 time to evaluate : 0.168 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 20 average time/residue: 0.1713 time to fit residues: 3.9468 Evaluate side-chains 20 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 18 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 407 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 0.0060 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 0.4980 chunk 17 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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: 0.7676 moved from start: 0.4897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 1528 Z= 0.343 Angle : 0.535 4.458 2084 Z= 0.286 Chirality : 0.046 0.132 223 Planarity : 0.004 0.028 269 Dihedral : 5.379 33.458 238 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.44 % Allowed : 11.51 % 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: -1.51 (0.54), residues: 192 helix: -2.57 (0.78), residues: 32 sheet: 1.60 (0.90), residues: 37 loop : -1.48 (0.45), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 436 PHE 0.011 0.002 PHE E 429 TYR 0.010 0.001 TYR E 396 ARG 0.002 0.001 ARG E 457 *********************** 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 29 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 27 time to evaluate : 0.170 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 27 average time/residue: 0.1969 time to fit residues: 5.9117 Evaluate side-chains 25 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 407 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 7 optimal weight: 0.0570 chunk 5 optimal weight: 0.0980 chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 0.3980 chunk 9 optimal weight: 0.9980 chunk 1 optimal weight: 0.0970 overall best weight: 0.2496 ------------------------------------------------------------------------------- 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: 0.7635 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1528 Z= 0.175 Angle : 0.453 3.785 2084 Z= 0.241 Chirality : 0.043 0.128 223 Planarity : 0.004 0.029 269 Dihedral : 4.849 31.140 238 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.72 % Allowed : 12.95 % 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: -1.45 (0.53), residues: 192 helix: -2.42 (0.79), residues: 32 sheet: 1.53 (0.88), residues: 37 loop : -1.43 (0.44), 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 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 23 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.172 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 22 average time/residue: 0.1945 time to fit residues: 4.9442 Evaluate side-chains 23 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 367 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 14 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.0070 chunk 7 optimal weight: 0.9980 chunk 13 optimal weight: 0.0770 chunk 5 optimal weight: 0.0970 chunk 15 optimal weight: 0.2980 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 0.0870 chunk 8 optimal weight: 0.8980 overall best weight: 0.1132 ------------------------------------------------------------------------------- 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: 0.7580 moved from start: 0.5226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 1528 Z= 0.107 Angle : 0.414 3.124 2084 Z= 0.220 Chirality : 0.042 0.120 223 Planarity : 0.003 0.030 269 Dihedral : 4.310 28.795 238 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.44 % Allowed : 12.23 % 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: -0.83 (0.55), residues: 192 helix: -1.91 (0.97), residues: 26 sheet: 1.71 (0.87), residues: 37 loop : -1.00 (0.46), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 436 PHE 0.005 0.001 PHE E 400 TYR 0.005 0.001 TYR E 351 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 26 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.181 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 24 average time/residue: 0.1999 time to fit residues: 5.3787 Evaluate side-chains 24 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 367 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.0570 chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 0.1980 chunk 1 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 9 optimal weight: 0.0970 chunk 16 optimal weight: 0.4980 chunk 4 optimal weight: 0.0170 chunk 13 optimal weight: 0.3980 chunk 2 optimal weight: 0.9990 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: 0.7592 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 1528 Z= 0.124 Angle : 0.414 3.281 2084 Z= 0.219 Chirality : 0.042 0.123 223 Planarity : 0.003 0.030 269 Dihedral : 4.319 28.963 238 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.72 % Allowed : 14.39 % 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: -0.78 (0.55), residues: 192 helix: -1.69 (1.25), residues: 19 sheet: 1.74 (0.87), residues: 37 loop : -1.07 (0.44), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 436 PHE 0.005 0.001 PHE E 377 TYR 0.005 0.001 TYR E 351 ARG 0.002 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 22 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 21 time to evaluate : 0.179 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 21 average time/residue: 0.1956 time to fit residues: 4.6524 Evaluate side-chains 22 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 21 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 367 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 4 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 13 optimal weight: 0.3980 chunk 0 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 17 optimal weight: 0.3980 chunk 12 optimal weight: 0.3980 chunk 11 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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: 0.7671 moved from start: 0.5364 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= 0.288 Angle : 0.489 4.596 2084 Z= 0.257 Chirality : 0.045 0.134 223 Planarity : 0.004 0.028 269 Dihedral : 5.050 33.013 238 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.72 % Allowed : 14.39 % 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: -1.40 (0.54), residues: 192 helix: -2.11 (0.86), residues: 32 sheet: 1.48 (0.86), residues: 37 loop : -1.45 (0.45), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 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 509 *********************** 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 25 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.174 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 24 average time/residue: 0.1819 time to fit residues: 4.9599 Evaluate side-chains 24 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 367 VAL 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: 0.2980 chunk 18 optimal weight: 0.4980 chunk 0 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 4 optimal weight: 0.1980 chunk 15 optimal weight: 0.6980 chunk 17 optimal weight: 0.2980 chunk 8 optimal weight: 0.2980 chunk 1 optimal weight: 0.3980 overall best weight: 0.2980 ------------------------------------------------------------------------------- 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: 0.5415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1528 Z= 0.208 Angle : 0.479 4.117 2084 Z= 0.252 Chirality : 0.044 0.131 223 Planarity : 0.004 0.028 269 Dihedral : 5.003 31.975 238 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.72 % Allowed : 15.11 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.54), residues: 192 helix: -2.13 (0.85), residues: 32 sheet: 1.43 (0.86), residues: 37 loop : -1.42 (0.45), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 436 PHE 0.006 0.001 PHE E 497 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 24 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.163 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 23 average time/residue: 0.1874 time to fit residues: 4.8734 Evaluate side-chains 24 residues out of total 167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 367 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 4 optimal weight: 0.4980 chunk 12 optimal weight: 0.0980 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 9 optimal weight: 0.0980 chunk 0 optimal weight: 0.9980 chunk 1 optimal weight: 0.1980 chunk 18 optimal weight: 0.0060 chunk 13 optimal weight: 0.0770 chunk 15 optimal weight: 0.4980 chunk 17 optimal weight: 0.0870 overall best weight: 0.0732 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.155796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.144626 restraints weight = 2087.200| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.41 r_work: 0.3507 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.5486 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= 0.098 Angle : 0.415 3.190 2084 Z= 0.220 Chirality : 0.042 0.122 223 Planarity : 0.003 0.029 269 Dihedral : 4.306 26.952 238 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.72 % Allowed : 14.39 % 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: -0.86 (0.55), residues: 192 helix: -1.69 (1.27), residues: 19 sheet: 1.66 (0.86), residues: 37 loop : -1.12 (0.45), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 436 PHE 0.005 0.001 PHE E 400 TYR 0.004 0.001 TYR E 351 ARG 0.002 0.000 ARG E 457 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1363.33 seconds wall clock time: 25 minutes 38.86 seconds (1538.86 seconds total)