Starting phenix.real_space_refine on Mon Feb 10 21:18:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mji_23874/02_2025/7mji_23874.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mji_23874/02_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_23874/02_2025/7mji_23874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mji_23874/02_2025/7mji_23874.map" model { file = "/net/cci-nas-00/data/ceres_data/7mji_23874/02_2025/7mji_23874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mji_23874/02_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-5592/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: 3.13, per 1000 atoms: 1.24 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 297.5 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: 0.36 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: 0.74 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: 2.620 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.420 Find NCS groups from input model: 0.020 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:12.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.420 ------------------------------------------------------------------------------- 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 : 0.269 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 1.0359 time to fit residues: 78.6318 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 : 0.288 ------------------------------------------------------------------------------- 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 = 0.085117 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: 0.8317 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 : 0.295 Fit side-chains REVERT: B 360 ASN cc_start: 0.8767 (OUTLIER) cc_final: 0.8496 (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: 0.8385 (p) outliers start: 9 outliers final: 4 residues processed: 74 average time/residue: 0.9391 time to fit residues: 71.5409 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 : 0.283 ------------------------------------------------------------------------------- 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: 0.9980 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 9 optimal weight: 0.0570 chunk 13 optimal weight: 1.9990 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: 0.6980 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 = 0.3373 r_free = 0.3373 target = 0.096430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.085360 restraints weight = 4143.957| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.50 r_work: 0.3075 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2586 Z= 0.218 Angle : 0.502 4.342 3515 Z= 0.262 Chirality : 0.043 0.128 374 Planarity : 0.003 0.027 458 Dihedral : 5.109 40.399 380 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.68 % Allowed : 13.97 % Favored : 82.35 % 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: -0.04 (0.47), residues: 316 helix: -3.55 (0.70), residues: 28 sheet: 0.65 (0.56), residues: 89 loop : 0.31 (0.43), 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 0.005 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 84 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.269 Fit side-chains REVERT: E 42 SER cc_start: 0.8576 (m) cc_final: 0.8305 (p) outliers start: 10 outliers final: 4 residues processed: 78 average time/residue: 0.9746 time to fit residues: 78.1131 Evaluate side-chains 69 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0570 chunk 18 optimal weight: 0.0980 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 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: 0.1980 chunk 29 optimal weight: 0.9980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 370 ASN B 409 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.095902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.084927 restraints weight = 4392.175| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.61 r_work: 0.3097 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2586 Z= 0.170 Angle : 0.493 4.570 3515 Z= 0.257 Chirality : 0.043 0.149 374 Planarity : 0.003 0.029 458 Dihedral : 4.863 37.901 380 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.21 % Allowed : 15.44 % Favored : 82.35 % 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 (0.47), residues: 316 helix: -3.23 (0.83), residues: 28 sheet: 0.27 (0.55), residues: 84 loop : 0.54 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.001 0.000 HIS B 519 PHE 0.007 0.001 PHE B 377 TYR 0.010 0.001 TYR B 495 ARG 0.006 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 77 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.307 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 72 average time/residue: 0.9673 time to fit residues: 71.7151 Evaluate side-chains 73 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=3.50 ------------------------------------------------------------------------------- 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: 0.0870 chunk 26 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.0370 chunk 9 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 overall best weight: 0.4036 ------------------------------------------------------------------------------- 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 = 0.3366 r_free = 0.3366 target = 0.096097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.084978 restraints weight = 4395.213| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.65 r_work: 0.3094 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2718 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= 0.166 Angle : 0.491 4.990 3515 Z= 0.256 Chirality : 0.043 0.136 374 Planarity : 0.003 0.024 458 Dihedral : 4.817 37.630 380 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.84 % Allowed : 16.18 % 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: -0.02 (0.46), residues: 316 helix: -3.39 (1.06), residues: 21 sheet: 0.09 (0.54), residues: 84 loop : 0.44 (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 0.006 0.001 PHE B 392 TYR 0.015 0.001 TYR B 365 ARG 0.005 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 76 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.297 Fit side-chains REVERT: B 360 ASN cc_start: 0.8790 (t0) cc_final: 0.8507 (t0) REVERT: B 424 LYS cc_start: 0.9041 (tptp) cc_final: 0.8621 (tppp) REVERT: E 119 ASP cc_start: 0.8680 (m-30) cc_final: 0.8427 (m-30) REVERT: E 132 MET cc_start: 0.8774 (mmt) cc_final: 0.7969 (mmt) outliers start: 5 outliers final: 5 residues processed: 72 average time/residue: 0.9593 time to fit residues: 71.1494 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 : 0.294 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3300 r_free = 0.3300 target = 0.091904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.080774 restraints weight = 4465.349| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.66 r_work: 0.3025 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 2586 Z= 0.386 Angle : 0.579 6.549 3515 Z= 0.298 Chirality : 0.045 0.149 374 Planarity : 0.003 0.025 458 Dihedral : 5.877 49.644 380 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.68 % Allowed : 15.44 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.46), residues: 316 helix: -2.92 (0.92), residues: 28 sheet: -0.17 (0.55), residues: 82 loop : 0.43 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 57 HIS 0.002 0.002 HIS B 519 PHE 0.013 0.001 PHE B 515 TYR 0.013 0.001 TYR B 495 ARG 0.004 0.001 ARG E 59 *********************** 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 80 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.305 Fit side-chains REVERT: B 360 ASN cc_start: 0.8936 (t0) cc_final: 0.8632 (t0) REVERT: E 77 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.7960 (ptp90) outliers start: 10 outliers final: 8 residues processed: 74 average time/residue: 0.9720 time to fit residues: 73.9941 Evaluate side-chains 72 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 392 PHE 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 126 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: 0.6980 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 0 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3322 r_free = 0.3322 target = 0.093274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.082069 restraints weight = 4504.666| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.68 r_work: 0.3047 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2933 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= 0.253 Angle : 0.534 6.573 3515 Z= 0.276 Chirality : 0.044 0.138 374 Planarity : 0.003 0.027 458 Dihedral : 5.464 44.622 380 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.68 % Allowed : 16.91 % Favored : 79.41 % 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: -2.84 (0.92), residues: 28 sheet: -0.20 (0.55), residues: 82 loop : 0.47 (0.43), residues: 206 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 0.010 0.001 PHE B 392 TYR 0.011 0.001 TYR B 495 ARG 0.006 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 75 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.317 Fit side-chains REVERT: B 360 ASN cc_start: 0.8975 (t0) cc_final: 0.8638 (t0) outliers start: 10 outliers final: 7 residues processed: 72 average time/residue: 0.9664 time to fit residues: 71.6786 Evaluate side-chains 70 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 514 SER 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: 1.9990 chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3334 r_free = 0.3334 target = 0.093932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.082851 restraints weight = 4357.302| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.63 r_work: 0.3058 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2586 Z= 0.224 Angle : 0.526 7.027 3515 Z= 0.270 Chirality : 0.044 0.135 374 Planarity : 0.003 0.027 458 Dihedral : 5.289 43.153 380 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.04 % Allowed : 18.38 % 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: -0.07 (0.47), residues: 316 helix: -2.79 (0.93), residues: 28 sheet: -0.05 (0.55), residues: 84 loop : 0.53 (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 0.006 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 75 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.317 Fit side-chains REVERT: B 360 ASN cc_start: 0.8988 (t0) cc_final: 0.8645 (t0) REVERT: E 85 LYS cc_start: 0.7768 (tttm) cc_final: 0.7389 (mtpm) outliers start: 11 outliers final: 9 residues processed: 73 average time/residue: 0.8849 time to fit residues: 66.6139 Evaluate side-chains 72 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 514 SER 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 126 SER Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 144 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 26 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 18 optimal weight: 0.0270 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.6438 ------------------------------------------------------------------------------- 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 = 0.3339 r_free = 0.3339 target = 0.094268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.083105 restraints weight = 4335.257| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.64 r_work: 0.3066 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3074 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= 0.222 Angle : 0.538 7.189 3515 Z= 0.278 Chirality : 0.044 0.135 374 Planarity : 0.004 0.029 458 Dihedral : 5.287 42.447 380 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 4.04 % Allowed : 19.12 % Favored : 76.84 % 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: -0.11 (0.47), residues: 316 helix: -3.08 (1.10), residues: 21 sheet: -0.06 (0.55), residues: 84 loop : 0.37 (0.43), residues: 211 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 0.016 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: 11 poor density : 64 time to evaluate : 0.293 Fit side-chains REVERT: B 360 ASN cc_start: 0.9010 (t0) cc_final: 0.8660 (t0) REVERT: E 85 LYS cc_start: 0.7766 (tttm) cc_final: 0.7386 (mtpm) REVERT: E 119 ASP cc_start: 0.8571 (m-30) cc_final: 0.8287 (m-30) REVERT: E 132 MET cc_start: 0.8716 (mmt) cc_final: 0.7842 (mmt) outliers start: 11 outliers final: 10 residues processed: 71 average time/residue: 0.8847 time to fit residues: 64.7786 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 : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 514 SER 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 Chi-restraints excluded: chain E residue 144 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 21 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 0.0570 chunk 18 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 1 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 = 0.3343 r_free = 0.3343 target = 0.094572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.083477 restraints weight = 4318.564| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.63 r_work: 0.3075 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3162 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= 0.214 Angle : 0.540 7.385 3515 Z= 0.278 Chirality : 0.044 0.136 374 Planarity : 0.004 0.029 458 Dihedral : 5.238 41.939 380 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.04 % Allowed : 19.49 % Favored : 76.47 % 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: -0.08 (0.47), residues: 316 helix: -3.08 (1.10), residues: 21 sheet: -0.03 (0.56), residues: 84 loop : 0.39 (0.43), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.001 0.001 HIS B 519 PHE 0.009 0.001 PHE B 515 TYR 0.016 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 74 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.256 Fit side-chains REVERT: B 360 ASN cc_start: 0.9002 (t0) cc_final: 0.8647 (t0) REVERT: E 27 GLU cc_start: 0.8568 (pm20) cc_final: 0.8270 (pm20) REVERT: E 85 LYS cc_start: 0.7747 (tttm) cc_final: 0.7379 (mtpm) REVERT: E 119 ASP cc_start: 0.8557 (m-30) cc_final: 0.8259 (m-30) REVERT: E 132 MET cc_start: 0.8709 (mmt) cc_final: 0.7831 (mmt) outliers start: 11 outliers final: 9 residues processed: 70 average time/residue: 0.9751 time to fit residues: 70.2591 Evaluate side-chains 71 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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 83 SER Chi-restraints excluded: chain E residue 86 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 144 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 0.0870 chunk 26 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 5 optimal weight: 0.0670 overall best weight: 0.4496 ------------------------------------------------------------------------------- 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 = 0.3358 r_free = 0.3358 target = 0.095545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.084337 restraints weight = 4362.299| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.65 r_work: 0.3094 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3177 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= 0.182 Angle : 0.532 7.292 3515 Z= 0.273 Chirality : 0.043 0.134 374 Planarity : 0.003 0.029 458 Dihedral : 5.101 40.001 380 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.31 % Allowed : 20.59 % 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: -0.05 (0.47), residues: 316 helix: -3.09 (1.09), residues: 21 sheet: 0.05 (0.57), residues: 82 loop : 0.39 (0.43), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.001 0.001 HIS B 519 PHE 0.007 0.001 PHE B 392 TYR 0.015 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: 2681.73 seconds wall clock time: 48 minutes 17.60 seconds (2897.60 seconds total)