Starting phenix.real_space_refine on Wed Mar 5 16:15:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mji_23874/03_2025/7mji_23874.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mji_23874/03_2025/7mji_23874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mji_23874/03_2025/7mji_23874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mji_23874/03_2025/7mji_23874.map" model { file = "/net/cci-nas-00/data/ceres_data/7mji_23874/03_2025/7mji_23874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mji_23874/03_2025/7mji_23874.cif" } resolution = 2.81 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= 0.024 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 14 5.16 5 C 1597 2.51 5 N 425 2.21 5 O 486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2522 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1547 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "E" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 961 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.80, per 1000 atoms: 1.11 Number of scatterers: 2522 At special positions: 0 Unit cell: (84, 59, 79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 486 8.00 N 425 7.00 C 1597 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 116 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 B1301 " - " ASN B 343 " Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 289.5 milliseconds 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 582 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 7 sheets defined 16.6% alpha, 37.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.648A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.555A pdb=" N GLU B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.614A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 53 removed outlier: 4.400A pdb=" N ASP E 52 " --> pdb=" O THR E 49 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR E 53 " --> pdb=" O PHE E 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 49 through 53' Processing helix chain 'E' and resid 84 through 86 No H-bonds generated for 'chain 'E' and resid 84 through 86' Processing helix chain 'E' and resid 107 through 111 removed outlier: 3.511A pdb=" N THR E 111 " --> pdb=" O ALA E 108 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.835A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.835A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'E' and resid 24 through 28 removed outlier: 3.644A pdb=" N LEU E 99 " --> pdb=" O CYS E 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 32 through 33 removed outlier: 6.611A pdb=" N MET E 55 " --> pdb=" O ARG E 71 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ARG E 71 " --> pdb=" O MET E 55 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TRP E 57 " --> pdb=" O ILE E 69 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 32 through 33 removed outlier: 4.140A pdb=" N VAL E 134 " --> pdb=" O ARG E 118 " (cutoff:3.500A) 88 hydrogen bonds defined for protein. 210 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: 0.67 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 813 1.34 - 1.46: 685 1.46 - 1.58: 1070 1.58 - 1.71: 0 1.71 - 1.83: 18 Bond restraints: 2586 Sorted by residual: bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.72e+00 bond pdb=" CG LEU E 41 " pdb=" CD1 LEU E 41 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.96e+00 bond pdb=" CB ASN B 360 " pdb=" CG ASN B 360 " ideal model delta sigma weight residual 1.516 1.556 -0.040 2.50e-02 1.60e+03 2.52e+00 bond pdb=" C TYR B 505 " pdb=" N GLN B 506 " ideal model delta sigma weight residual 1.340 1.266 0.074 5.87e-02 2.90e+02 1.58e+00 bond pdb=" CG1 ILE E 69 " pdb=" CD1 ILE E 69 " ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.58e+00 ... (remaining 2581 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 3354 1.81 - 3.63: 139 3.63 - 5.44: 18 5.44 - 7.25: 3 7.25 - 9.06: 1 Bond angle restraints: 3515 Sorted by residual: angle pdb=" CA ASN B 360 " pdb=" CB ASN B 360 " pdb=" CG ASN B 360 " ideal model delta sigma weight residual 112.60 115.23 -2.63 1.00e+00 1.00e+00 6.90e+00 angle pdb=" CA LEU E 84 " pdb=" CB LEU E 84 " pdb=" CG LEU E 84 " ideal model delta sigma weight residual 116.30 125.36 -9.06 3.50e+00 8.16e-02 6.71e+00 angle pdb=" C LYS E 96 " pdb=" N ASN E 97 " pdb=" CA ASN E 97 " ideal model delta sigma weight residual 122.36 125.96 -3.60 1.42e+00 4.96e-01 6.41e+00 angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 122.93 126.73 -3.80 1.51e+00 4.39e-01 6.33e+00 angle pdb=" CB ARG E 59 " pdb=" CG ARG E 59 " pdb=" CD ARG E 59 " ideal model delta sigma weight residual 111.30 116.91 -5.61 2.30e+00 1.89e-01 5.95e+00 ... (remaining 3510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.39: 1393 15.39 - 30.77: 110 30.77 - 46.15: 20 46.15 - 61.54: 6 61.54 - 76.92: 5 Dihedral angle restraints: 1534 sinusoidal: 610 harmonic: 924 Sorted by residual: dihedral pdb=" CA LEU B 517 " pdb=" C LEU B 517 " pdb=" N LEU B 518 " pdb=" CA LEU B 518 " ideal model delta harmonic sigma weight residual 180.00 161.84 18.16 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA ARG B 403 " pdb=" C ARG B 403 " pdb=" N GLY B 404 " pdb=" CA GLY B 404 " ideal model delta harmonic sigma weight residual -180.00 -161.99 -18.01 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA PHE B 515 " pdb=" C PHE B 515 " pdb=" N GLU B 516 " pdb=" CA GLU B 516 " ideal model delta harmonic sigma weight residual 180.00 162.13 17.87 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 1531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 175 0.032 - 0.063: 114 0.063 - 0.095: 52 0.095 - 0.127: 26 0.127 - 0.158: 7 Chirality restraints: 374 Sorted by residual: chirality pdb=" CA VAL E 58 " pdb=" N VAL E 58 " pdb=" C VAL E 58 " pdb=" CB VAL E 58 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.27e-01 chirality pdb=" CA ILE B 358 " pdb=" N ILE B 358 " pdb=" C ILE B 358 " pdb=" CB ILE B 358 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.07e-01 chirality pdb=" CA ILE B 434 " pdb=" N ILE B 434 " pdb=" C ILE B 434 " pdb=" CB ILE B 434 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 ... (remaining 371 not shown) Planarity restraints: 459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET E 103 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.48e+00 pdb=" C MET E 103 " 0.040 2.00e-02 2.50e+03 pdb=" O MET E 103 " -0.015 2.00e-02 2.50e+03 pdb=" N ASN E 104 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS E 43 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.41e+00 pdb=" C CYS E 43 " -0.040 2.00e-02 2.50e+03 pdb=" O CYS E 43 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA E 44 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 520 " -0.036 5.00e-02 4.00e+02 5.49e-02 4.82e+00 pdb=" N PRO B 521 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 521 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 521 " -0.030 5.00e-02 4.00e+02 ... (remaining 456 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 917 2.87 - 3.38: 2025 3.38 - 3.89: 4248 3.89 - 4.39: 4808 4.39 - 4.90: 8495 Nonbonded interactions: 20493 Sorted by model distance: nonbonded pdb=" OG SER B 366 " pdb=" OD1 ASN B 388 " model vdw 2.367 3.040 nonbonded pdb=" NE ARG E 71 " pdb=" OD2 ASP E 119 " model vdw 2.373 3.120 nonbonded pdb=" NE2 GLN E 60 " pdb=" O LYS E 64 " model vdw 2.446 3.120 nonbonded pdb=" OH TYR B 489 " pdb=" NH2 ARG E 124 " model vdw 2.474 3.120 nonbonded pdb=" NE ARG B 457 " pdb=" OD2 ASP B 467 " model vdw 2.492 3.120 ... (remaining 20488 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 2.510 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.490 Find NCS groups from input model: 0.030 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:13.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 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 : 0.006 0.074 2586 Z= 0.385 Angle : 0.808 9.063 3515 Z= 0.427 Chirality : 0.053 0.158 374 Planarity : 0.008 0.070 458 Dihedral : 12.491 76.924 937 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.44), residues: 316 helix: -4.87 (0.21), residues: 27 sheet: 0.26 (0.55), residues: 93 loop : -0.23 (0.39), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 68 HIS 0.002 0.001 HIS B 519 PHE 0.017 0.002 PHE B 377 TYR 0.021 0.002 TYR B 495 ARG 0.017 0.002 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.257 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.9994 time to fit residues: 75.8694 Evaluate side-chains 63 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 26 optimal weight: 2.9990 chunk 23 optimal weight: 0.0870 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 0.1980 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.096624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.085116 restraints weight = 4346.347| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.66 r_work: 0.3100 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2586 Z= 0.192 Angle : 0.511 4.386 3515 Z= 0.266 Chirality : 0.042 0.131 374 Planarity : 0.004 0.030 458 Dihedral : 5.144 38.342 380 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.31 % Allowed : 11.76 % Favored : 84.93 % 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: -0.18 (0.47), residues: 316 helix: -4.14 (0.44), residues: 28 sheet: 0.58 (0.54), residues: 99 loop : 0.27 (0.45), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 57 HIS 0.001 0.000 HIS B 519 PHE 0.009 0.001 PHE B 377 TYR 0.013 0.001 TYR B 365 ARG 0.006 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.292 Fit side-chains REVERT: B 360 ASN cc_start: 0.8769 (OUTLIER) cc_final: 0.8498 (t0) REVERT: B 394 ASN cc_start: 0.7347 (m-40) cc_final: 0.7060 (p0) REVERT: E 42 SER cc_start: 0.8664 (m) cc_final: 0.8384 (p) outliers start: 9 outliers final: 4 residues processed: 74 average time/residue: 0.9320 time to fit residues: 71.0151 Evaluate side-chains 72 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 9 optimal weight: 0.0570 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN B 370 ASN B 388 ASN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.094832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.083532 restraints weight = 4383.210| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.67 r_work: 0.3071 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2586 Z= 0.232 Angle : 0.507 4.522 3515 Z= 0.263 Chirality : 0.043 0.127 374 Planarity : 0.003 0.027 458 Dihedral : 5.176 41.167 380 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.68 % Allowed : 14.34 % Favored : 81.99 % 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: -0.05 (0.47), residues: 316 helix: -3.54 (0.70), residues: 28 sheet: 0.63 (0.56), residues: 89 loop : 0.30 (0.44), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.001 0.001 HIS B 519 PHE 0.008 0.001 PHE B 377 TYR 0.012 0.001 TYR B 495 ARG 0.006 0.001 ARG E 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.252 Fit side-chains REVERT: B 360 ASN cc_start: 0.8592 (OUTLIER) cc_final: 0.8365 (t0) REVERT: E 42 SER cc_start: 0.8533 (m) cc_final: 0.8256 (p) outliers start: 10 outliers final: 4 residues processed: 80 average time/residue: 1.0429 time to fit residues: 85.8299 Evaluate side-chains 74 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 20 optimal weight: 0.0980 chunk 18 optimal weight: 0.0010 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 29 optimal weight: 0.0870 overall best weight: 0.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN B 370 ASN B 409 GLN B 414 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.095935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.084805 restraints weight = 4387.099| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.67 r_work: 0.3094 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2586 Z= 0.158 Angle : 0.493 4.663 3515 Z= 0.258 Chirality : 0.043 0.151 374 Planarity : 0.003 0.027 458 Dihedral : 4.850 37.604 380 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.57 % Allowed : 16.18 % Favored : 81.25 % 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: 0.02 (0.46), residues: 316 helix: -3.24 (0.84), residues: 28 sheet: 0.38 (0.55), residues: 83 loop : 0.48 (0.43), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.001 0.001 HIS B 519 PHE 0.006 0.001 PHE B 377 TYR 0.009 0.001 TYR B 495 ARG 0.007 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.254 Fit side-chains REVERT: B 360 ASN cc_start: 0.8544 (OUTLIER) cc_final: 0.8322 (t0) REVERT: B 424 LYS cc_start: 0.9005 (tptp) cc_final: 0.8624 (tppp) outliers start: 7 outliers final: 4 residues processed: 73 average time/residue: 0.9155 time to fit residues: 68.8289 Evaluate side-chains 74 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 30 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 0.0170 chunk 26 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.0980 chunk 9 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.096040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.084857 restraints weight = 4404.024| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.67 r_work: 0.3093 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2586 Z= 0.171 Angle : 0.495 5.222 3515 Z= 0.258 Chirality : 0.043 0.136 374 Planarity : 0.003 0.025 458 Dihedral : 4.830 37.711 380 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.94 % Allowed : 15.81 % Favored : 81.25 % 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: -0.06 (0.46), residues: 316 helix: -3.42 (1.05), residues: 21 sheet: 0.08 (0.54), residues: 84 loop : 0.41 (0.43), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.001 0.001 HIS B 519 PHE 0.007 0.001 PHE B 392 TYR 0.009 0.001 TYR B 495 ARG 0.006 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.295 Fit side-chains REVERT: B 360 ASN cc_start: 0.8511 (OUTLIER) cc_final: 0.8289 (t0) REVERT: B 424 LYS cc_start: 0.9049 (tptp) cc_final: 0.8677 (tppp) REVERT: E 119 ASP cc_start: 0.8688 (m-30) cc_final: 0.8431 (m-30) REVERT: E 132 MET cc_start: 0.8793 (mmt) cc_final: 0.7990 (mmt) outliers start: 8 outliers final: 7 residues processed: 73 average time/residue: 0.9503 time to fit residues: 71.5080 Evaluate side-chains 78 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 15 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.092453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.081304 restraints weight = 4460.327| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.66 r_work: 0.3032 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 2586 Z= 0.348 Angle : 0.562 6.374 3515 Z= 0.290 Chirality : 0.045 0.147 374 Planarity : 0.003 0.026 458 Dihedral : 5.632 47.218 380 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.68 % Allowed : 16.54 % Favored : 79.78 % 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: -0.19 (0.46), residues: 316 helix: -2.88 (0.94), residues: 28 sheet: -0.16 (0.55), residues: 82 loop : 0.44 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 57 HIS 0.002 0.001 HIS B 519 PHE 0.012 0.001 PHE B 515 TYR 0.019 0.001 TYR B 365 ARG 0.004 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.257 Fit side-chains REVERT: E 77 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.7938 (ptp90) outliers start: 10 outliers final: 7 residues processed: 74 average time/residue: 0.8942 time to fit residues: 67.9998 Evaluate side-chains 77 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 chunk 24 optimal weight: 0.4980 chunk 25 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3331 r_free = 0.3331 target = 0.094144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.082904 restraints weight = 4506.434| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.68 r_work: 0.3057 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2586 Z= 0.219 Angle : 0.521 6.228 3515 Z= 0.272 Chirality : 0.044 0.135 374 Planarity : 0.003 0.028 458 Dihedral : 5.249 42.792 380 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.31 % Allowed : 18.38 % Favored : 78.31 % 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: -0.13 (0.47), residues: 316 helix: -2.83 (0.93), residues: 28 sheet: -0.12 (0.54), residues: 84 loop : 0.48 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 68 HIS 0.001 0.001 HIS B 519 PHE 0.009 0.001 PHE B 515 TYR 0.014 0.001 TYR B 365 ARG 0.007 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.292 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 74 average time/residue: 0.8980 time to fit residues: 68.4282 Evaluate side-chains 76 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3317 r_free = 0.3317 target = 0.093182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.082080 restraints weight = 4373.602| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.64 r_work: 0.3046 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 2586 Z= 0.270 Angle : 0.539 6.970 3515 Z= 0.278 Chirality : 0.044 0.137 374 Planarity : 0.003 0.027 458 Dihedral : 5.416 44.937 380 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.41 % Allowed : 17.65 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.47), residues: 316 helix: -2.80 (0.92), residues: 28 sheet: -0.09 (0.55), residues: 84 loop : 0.47 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 68 HIS 0.002 0.001 HIS B 519 PHE 0.011 0.001 PHE B 515 TYR 0.014 0.001 TYR B 365 ARG 0.007 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.258 Fit side-chains REVERT: E 119 ASP cc_start: 0.8607 (m-30) cc_final: 0.8322 (m-30) REVERT: E 132 MET cc_start: 0.8683 (mmt) cc_final: 0.7773 (mmt) outliers start: 12 outliers final: 10 residues processed: 73 average time/residue: 0.9415 time to fit residues: 70.6242 Evaluate side-chains 73 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 26 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3323 r_free = 0.3323 target = 0.093442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.082322 restraints weight = 4343.298| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.64 r_work: 0.3049 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 2586 Z= 0.266 Angle : 0.558 7.288 3515 Z= 0.289 Chirality : 0.044 0.137 374 Planarity : 0.004 0.028 458 Dihedral : 5.470 44.674 380 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.41 % Allowed : 18.01 % Favored : 77.57 % 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: -0.16 (0.47), residues: 316 helix: -2.76 (0.93), residues: 28 sheet: -0.12 (0.55), residues: 84 loop : 0.45 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 68 HIS 0.001 0.001 HIS B 519 PHE 0.009 0.001 PHE B 515 TYR 0.014 0.001 TYR B 365 ARG 0.007 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.366 Fit side-chains REVERT: E 119 ASP cc_start: 0.8602 (m-30) cc_final: 0.8296 (m-30) REVERT: E 132 MET cc_start: 0.8701 (mmt) cc_final: 0.7799 (mmt) outliers start: 12 outliers final: 10 residues processed: 71 average time/residue: 0.9339 time to fit residues: 68.2942 Evaluate side-chains 73 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain E residue 55 MET Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 21 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 0.1980 chunk 1 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3346 r_free = 0.3346 target = 0.094749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.083663 restraints weight = 4316.061| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.62 r_work: 0.3075 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2586 Z= 0.200 Angle : 0.527 7.325 3515 Z= 0.273 Chirality : 0.043 0.136 374 Planarity : 0.004 0.028 458 Dihedral : 5.148 40.975 380 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.31 % Allowed : 19.49 % Favored : 77.21 % 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: -0.13 (0.47), residues: 316 helix: -3.11 (1.08), residues: 21 sheet: -0.03 (0.56), residues: 84 loop : 0.34 (0.43), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.001 0.001 HIS B 519 PHE 0.008 0.001 PHE B 515 TYR 0.012 0.001 TYR B 365 ARG 0.007 0.001 ARG B 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.282 Fit side-chains REVERT: E 27 GLU cc_start: 0.8677 (pm20) cc_final: 0.8441 (pm20) outliers start: 9 outliers final: 8 residues processed: 69 average time/residue: 0.9514 time to fit residues: 67.5739 Evaluate side-chains 70 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 21 optimal weight: 0.2980 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 12 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.094391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.083249 restraints weight = 4356.474| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.65 r_work: 0.3072 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2586 Z= 0.215 Angle : 0.538 7.338 3515 Z= 0.278 Chirality : 0.044 0.136 374 Planarity : 0.004 0.030 458 Dihedral : 5.234 41.995 380 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.94 % Allowed : 20.96 % Favored : 76.10 % 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: -0.06 (0.47), residues: 316 helix: -3.08 (1.09), residues: 21 sheet: 0.10 (0.57), residues: 82 loop : 0.35 (0.43), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 68 HIS 0.001 0.001 HIS B 519 PHE 0.007 0.001 PHE B 515 TYR 0.017 0.001 TYR B 365 ARG 0.007 0.001 ARG B 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2701.71 seconds wall clock time: 46 minutes 39.39 seconds (2799.39 seconds total)