Starting phenix.real_space_refine on Thu Sep 10 21:03:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uhg_64163/09_2026/9uhg_64163.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uhg_64163/09_2026/9uhg_64163.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uhg_64163/09_2026/9uhg_64163.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uhg_64163/09_2026/9uhg_64163.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uhg_64163/09_2026/9uhg_64163.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uhg_64163/09_2026/9uhg_64163.map" } resolution = 3.91 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 sd= 0.053 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 17 5.16 5 C 2133 2.51 5 N 562 2.21 5 O 648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3360 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1588 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 13, 'TRANS': 184} Chain: "I" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 901 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "M" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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: 1.02, per 1000 atoms: 0.30 Number of scatterers: 3360 At special positions: 0 Unit cell: (62.06, 89.88, 97.37, 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 17 16.00 O 648 8.00 N 562 7.00 C 2133 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 95 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 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 BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A 601 " - " ASN A 354 " " NAG B 1 " - " ASN A 343 " Time building additional restraints: 0.28 Conformation dependent library (CDL) restraints added in 135.8 milliseconds 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 774 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 7 sheets defined 7.8% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.798A pdb=" N ASN A 343 " --> pdb=" O GLU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 372 removed outlier: 4.096A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.604A pdb=" N ASN I 32 " --> pdb=" O VAL I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 64 removed outlier: 3.749A pdb=" N LYS I 64 " --> pdb=" O ASP I 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 61 through 64' Processing helix chain 'M' and resid 79 through 83 removed outlier: 4.172A pdb=" N ILE M 83 " --> pdb=" O PRO M 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.189A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG A 509 " --> pdb=" O TRP A 436 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR A 430 " --> pdb=" O PHE A 515 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.738A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER I 25 " --> pdb=" O GLN I 3 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER I 7 " --> pdb=" O SER I 21 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER I 21 " --> pdb=" O SER I 7 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR I 77 " --> pdb=" O ASP I 72 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASP I 72 " --> pdb=" O THR I 77 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR I 79 " --> pdb=" O SER I 70 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR I 68 " --> pdb=" O GLN I 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.532A pdb=" N THR I 113 " --> pdb=" O TYR I 93 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N MET I 34 " --> pdb=" O LEU I 50 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LEU I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG I 38 " --> pdb=" O GLU I 46 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLU I 46 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 4 through 7 removed outlier: 4.325A pdb=" N VAL M 19 " --> pdb=" O ILE M 75 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE M 75 " --> pdb=" O VAL M 19 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER M 63 " --> pdb=" O THR M 74 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 10 through 12 removed outlier: 3.613A pdb=" N GLU M 105 " --> pdb=" O LEU M 11 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 10 through 12 removed outlier: 3.613A pdb=" N GLU M 105 " --> pdb=" O LEU M 11 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN M 90 " --> pdb=" O ALA M 97 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALA M 97 " --> pdb=" O GLN M 90 " (cutoff:3.500A) 71 hydrogen bonds defined for protein. 165 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: 0.35 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1066 1.34 - 1.46: 902 1.46 - 1.58: 1456 1.58 - 1.70: 0 1.70 - 1.82: 22 Bond restraints: 3446 Sorted by residual: bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.70e+00 bond pdb=" C5 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.36e+00 bond pdb=" C5 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.16e+00 bond pdb=" C5 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.16e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.427 -0.021 2.00e-02 2.50e+03 1.16e+00 ... (remaining 3441 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 4512 1.35 - 2.69: 127 2.69 - 4.04: 31 4.04 - 5.39: 6 5.39 - 6.73: 2 Bond angle restraints: 4678 Sorted by residual: angle pdb=" N ILE M 29 " pdb=" CA ILE M 29 " pdb=" C ILE M 29 " ideal model delta sigma weight residual 113.10 108.11 4.99 9.70e-01 1.06e+00 2.65e+01 angle pdb=" C ASN M 30 " pdb=" CA ASN M 30 " pdb=" CB ASN M 30 " ideal model delta sigma weight residual 116.34 110.63 5.71 1.40e+00 5.10e-01 1.67e+01 angle pdb=" N ILE M 31 " pdb=" CA ILE M 31 " pdb=" C ILE M 31 " ideal model delta sigma weight residual 113.07 109.81 3.26 1.37e+00 5.33e-01 5.65e+00 angle pdb=" N ASN M 30 " pdb=" CA ASN M 30 " pdb=" C ASN M 30 " ideal model delta sigma weight residual 108.00 111.47 -3.47 1.48e+00 4.57e-01 5.48e+00 angle pdb=" C GLN I 13 " pdb=" CA GLN I 13 " pdb=" CB GLN I 13 " ideal model delta sigma weight residual 109.42 113.06 -3.64 1.57e+00 4.06e-01 5.36e+00 ... (remaining 4673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.27: 1855 16.27 - 32.54: 163 32.54 - 48.81: 41 48.81 - 65.08: 4 65.08 - 81.35: 6 Dihedral angle restraints: 2069 sinusoidal: 846 harmonic: 1223 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 30.25 62.75 1 1.00e+01 1.00e-02 5.20e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 136.98 -43.98 1 1.00e+01 1.00e-02 2.69e+01 dihedral pdb=" CA CYS A 488 " pdb=" C CYS A 488 " pdb=" N TYR A 489 " pdb=" CA TYR A 489 " ideal model delta harmonic sigma weight residual -180.00 -163.24 -16.76 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 2066 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 455 0.081 - 0.161: 50 0.161 - 0.242: 1 0.242 - 0.323: 0 0.323 - 0.403: 1 Chirality restraints: 507 Sorted by residual: chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" CB ILE A 468 " pdb=" CA ILE A 468 " pdb=" CG1 ILE A 468 " pdb=" CG2 ILE A 468 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CB THR A 470 " pdb=" CA THR A 470 " pdb=" OG1 THR A 470 " pdb=" CG2 THR A 470 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.71e-01 ... (remaining 504 not shown) Planarity restraints: 602 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER M 7 " 0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO M 8 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO M 8 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO M 8 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA M 43 " 0.017 5.00e-02 4.00e+02 2.64e-02 1.11e+00 pdb=" N PRO M 44 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO M 44 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO M 44 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN M 79 " 0.016 5.00e-02 4.00e+02 2.39e-02 9.18e-01 pdb=" N PRO M 80 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO M 80 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO M 80 " 0.013 5.00e-02 4.00e+02 ... (remaining 599 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 217 2.73 - 3.27: 3329 3.27 - 3.82: 4955 3.82 - 4.36: 5393 4.36 - 4.90: 9628 Nonbonded interactions: 23522 Sorted by model distance: nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.191 3.040 nonbonded pdb=" OG1 THR A 430 " pdb=" O PHE A 515 " model vdw 2.289 3.040 nonbonded pdb=" NE2 GLN A 474 " pdb=" O GLY A 476 " model vdw 2.325 3.120 nonbonded pdb=" O VAL I 5 " pdb=" OG1 THR I 23 " model vdw 2.329 3.040 nonbonded pdb=" OD1 ASP I 72 " pdb=" OG1 THR I 77 " model vdw 2.338 3.040 ... (remaining 23517 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 group one per residue 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: 1.340 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.620 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3454 Z= 0.136 Angle : 0.605 6.733 4697 Z= 0.321 Chirality : 0.048 0.403 507 Planarity : 0.004 0.035 600 Dihedral : 13.480 81.353 1280 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.39), residues: 418 helix: -4.62 (0.91), residues: 12 sheet: -0.13 (0.48), residues: 123 loop : -1.51 (0.35), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 498 TYR 0.010 0.001 TYR A 453 PHE 0.011 0.001 PHE A 377 TRP 0.011 0.001 TRP A 353 HIS 0.004 0.001 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 ( 3446) covalent geometry : angle 0.59109 / 0.32 ( 4678) SS BOND : bond 0.00249 / 0.18 ( 5) SS BOND : angle 1.19202 / 0.61 ( 10) hydrogen bonds : bond 0.30061 / 18.60 ( 68) hydrogen bonds : angle 11.03147 / 7.55 ( 165) link_BETA1-4 : bond 0.00009 / 0.00 ( 1) link_BETA1-4 : angle 2.69735 / 1.42 ( 3) link_NAG-ASN : bond 0.00510 / 0.27 ( 2) link_NAG-ASN : angle 2.91168 / 1.69 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.118 Fit side-chains revert: symmetry clash REVERT: A 467 ASP cc_start: 0.5997 (t0) cc_final: 0.5773 (t0) REVERT: A 518 LEU cc_start: 0.7711 (tp) cc_final: 0.7409 (tp) REVERT: I 88 GLU cc_start: 0.7672 (pm20) cc_final: 0.7437 (pm20) REVERT: I 94 TYR cc_start: 0.8242 (m-80) cc_final: 0.7962 (m-80) REVERT: M 58 VAL cc_start: 0.8667 (t) cc_final: 0.8453 (t) REVERT: M 78 LEU cc_start: 0.8032 (mt) cc_final: 0.7650 (mp) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.0779 time to fit residues: 9.2295 Evaluate side-chains 80 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.0470 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.0010 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 overall best weight: 0.4886 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.125121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.106945 restraints weight = 8688.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.109966 restraints weight = 5060.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.112036 restraints weight = 3423.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.113509 restraints weight = 2561.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.114493 restraints weight = 2049.299| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3454 Z= 0.116 Angle : 0.642 5.645 4697 Z= 0.322 Chirality : 0.045 0.153 507 Planarity : 0.004 0.027 600 Dihedral : 4.941 28.180 531 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 1.65 % Allowed : 11.54 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.39), residues: 418 helix: -5.45 (0.27), residues: 6 sheet: 0.14 (0.47), residues: 121 loop : -1.38 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 61 TYR 0.016 0.001 TYR A 495 PHE 0.014 0.001 PHE A 374 TRP 0.006 0.001 TRP A 353 HIS 0.002 0.001 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 ( 3446) covalent geometry : angle 0.63088 / 0.32 ( 4678) SS BOND : bond 0.00287 / 0.20 ( 5) SS BOND : angle 0.97658 / 0.52 ( 10) hydrogen bonds : bond 0.04633 / 3.08 ( 68) hydrogen bonds : angle 7.87146 / 5.26 ( 165) link_BETA1-4 : bond 0.00230 / 0.12 ( 1) link_BETA1-4 : angle 1.83055 / 0.96 ( 3) link_NAG-ASN : bond 0.00360 / 0.18 ( 2) link_NAG-ASN : angle 2.97999 / 1.70 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.137 Fit side-chains REVERT: A 448 ASN cc_start: 0.8254 (t0) cc_final: 0.7996 (t0) REVERT: A 481 LYS cc_start: 0.7727 (ptpp) cc_final: 0.7479 (tppt) REVERT: I 86 ARG cc_start: 0.7794 (mpp80) cc_final: 0.7536 (mpp80) REVERT: I 88 GLU cc_start: 0.7689 (pm20) cc_final: 0.7293 (pm20) REVERT: I 90 THR cc_start: 0.8509 (p) cc_final: 0.8049 (t) REVERT: M 55 GLU cc_start: 0.8394 (tp30) cc_final: 0.8115 (tp30) REVERT: M 78 LEU cc_start: 0.8048 (mt) cc_final: 0.7736 (mp) outliers start: 6 outliers final: 6 residues processed: 87 average time/residue: 0.0713 time to fit residues: 7.5228 Evaluate side-chains 83 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain M residue 9 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 19 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 0.0670 chunk 5 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.125104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.107198 restraints weight = 8817.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.110158 restraints weight = 5230.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.112196 restraints weight = 3557.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.113553 restraints weight = 2668.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.114567 restraints weight = 2152.699| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3454 Z= 0.114 Angle : 0.629 6.930 4697 Z= 0.310 Chirality : 0.044 0.154 507 Planarity : 0.004 0.029 600 Dihedral : 4.604 16.713 531 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 2.75 % Allowed : 14.84 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.39), residues: 418 helix: -5.45 (0.27), residues: 6 sheet: 0.30 (0.47), residues: 125 loop : -1.44 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 346 TYR 0.012 0.001 TYR I 58 PHE 0.013 0.001 PHE A 374 TRP 0.006 0.001 TRP A 353 HIS 0.004 0.001 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 ( 3446) covalent geometry : angle 0.62098 / 0.31 ( 4678) SS BOND : bond 0.00240 / 0.16 ( 5) SS BOND : angle 0.85068 / 0.45 ( 10) hydrogen bonds : bond 0.03763 / 2.50 ( 68) hydrogen bonds : angle 7.14897 / 4.68 ( 165) link_BETA1-4 : bond 0.00208 / 0.11 ( 1) link_BETA1-4 : angle 1.48919 / 0.79 ( 3) link_NAG-ASN : bond 0.00235 / 0.12 ( 2) link_NAG-ASN : angle 2.61760 / 1.47 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.136 Fit side-chains REVERT: A 448 ASN cc_start: 0.8356 (t0) cc_final: 0.8016 (t0) REVERT: A 467 ASP cc_start: 0.6138 (t0) cc_final: 0.5914 (t0) REVERT: A 481 LYS cc_start: 0.7749 (ptpp) cc_final: 0.7484 (tppt) REVERT: A 518 LEU cc_start: 0.7888 (tp) cc_final: 0.7674 (tp) REVERT: I 80 LEU cc_start: 0.7404 (tt) cc_final: 0.7112 (tt) REVERT: I 88 GLU cc_start: 0.7759 (pm20) cc_final: 0.7495 (pm20) REVERT: I 90 THR cc_start: 0.8317 (p) cc_final: 0.7891 (t) REVERT: I 116 THR cc_start: 0.9218 (m) cc_final: 0.8859 (p) REVERT: M 78 LEU cc_start: 0.8056 (mt) cc_final: 0.7746 (mp) outliers start: 10 outliers final: 8 residues processed: 85 average time/residue: 0.0760 time to fit residues: 7.8170 Evaluate side-chains 86 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain M residue 21 PHE Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 56 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 23 optimal weight: 4.9990 chunk 14 optimal weight: 0.3980 chunk 39 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.126140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.108548 restraints weight = 8654.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.111400 restraints weight = 5097.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.113413 restraints weight = 3485.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.114797 restraints weight = 2606.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.115760 restraints weight = 2096.044| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3454 Z= 0.121 Angle : 0.617 6.076 4697 Z= 0.306 Chirality : 0.044 0.188 507 Planarity : 0.004 0.031 600 Dihedral : 4.624 17.357 531 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 3.02 % Allowed : 17.31 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.39), residues: 418 helix: -5.45 (0.27), residues: 6 sheet: 0.46 (0.47), residues: 125 loop : -1.46 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 346 TYR 0.014 0.001 TYR A 453 PHE 0.018 0.002 PHE A 374 TRP 0.006 0.001 TRP A 353 HIS 0.005 0.001 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 3446) covalent geometry : angle 0.61088 / 0.31 ( 4678) SS BOND : bond 0.00276 / 0.19 ( 5) SS BOND : angle 0.76346 / 0.41 ( 10) hydrogen bonds : bond 0.03495 / 2.35 ( 68) hydrogen bonds : angle 6.76677 / 4.41 ( 165) link_BETA1-4 : bond 0.00059 / 0.03 ( 1) link_BETA1-4 : angle 1.30108 / 0.70 ( 3) link_NAG-ASN : bond 0.00190 / 0.09 ( 2) link_NAG-ASN : angle 2.32644 / 1.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.126 Fit side-chains REVERT: A 448 ASN cc_start: 0.8387 (t0) cc_final: 0.8066 (t0) REVERT: A 467 ASP cc_start: 0.6293 (t0) cc_final: 0.5965 (t0) REVERT: I 80 LEU cc_start: 0.7303 (tt) cc_final: 0.7054 (tt) REVERT: I 88 GLU cc_start: 0.7822 (pm20) cc_final: 0.7533 (pm20) REVERT: I 90 THR cc_start: 0.8290 (p) cc_final: 0.7872 (t) REVERT: I 116 THR cc_start: 0.9195 (m) cc_final: 0.8842 (p) REVERT: M 78 LEU cc_start: 0.8061 (mt) cc_final: 0.7770 (mp) outliers start: 11 outliers final: 7 residues processed: 89 average time/residue: 0.0683 time to fit residues: 7.4058 Evaluate side-chains 85 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain M residue 21 PHE Chi-restraints excluded: chain M residue 31 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 25 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.123601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.106464 restraints weight = 8798.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.109253 restraints weight = 5099.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.111208 restraints weight = 3460.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.112519 restraints weight = 2572.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.113464 restraints weight = 2060.321| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3454 Z= 0.156 Angle : 0.696 8.808 4697 Z= 0.340 Chirality : 0.044 0.179 507 Planarity : 0.004 0.039 600 Dihedral : 4.960 18.639 531 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 2.75 % Allowed : 19.51 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.39), residues: 418 helix: -5.46 (0.27), residues: 6 sheet: 0.36 (0.46), residues: 125 loop : -1.51 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 346 TYR 0.017 0.001 TYR A 453 PHE 0.021 0.002 PHE A 374 TRP 0.007 0.001 TRP A 353 HIS 0.007 0.002 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 3446) covalent geometry : angle 0.69201 / 0.34 ( 4678) SS BOND : bond 0.00358 / 0.23 ( 5) SS BOND : angle 0.80679 / 0.44 ( 10) hydrogen bonds : bond 0.03489 / 2.30 ( 68) hydrogen bonds : angle 6.69496 / 4.38 ( 165) link_BETA1-4 : bond 0.00083 / 0.04 ( 1) link_BETA1-4 : angle 1.09101 / 0.60 ( 3) link_NAG-ASN : bond 0.00217 / 0.10 ( 2) link_NAG-ASN : angle 2.14748 / 1.19 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.125 Fit side-chains REVERT: A 448 ASN cc_start: 0.8323 (t0) cc_final: 0.8096 (t0) REVERT: I 86 ARG cc_start: 0.7929 (mpp80) cc_final: 0.7617 (mpp80) REVERT: I 88 GLU cc_start: 0.7916 (pm20) cc_final: 0.7672 (pm20) REVERT: I 90 THR cc_start: 0.8285 (p) cc_final: 0.7830 (t) REVERT: I 116 THR cc_start: 0.9139 (m) cc_final: 0.8768 (p) REVERT: M 78 LEU cc_start: 0.8092 (mt) cc_final: 0.7785 (mp) REVERT: M 81 GLU cc_start: 0.8930 (mp0) cc_final: 0.7598 (tm-30) outliers start: 10 outliers final: 9 residues processed: 88 average time/residue: 0.0655 time to fit residues: 7.0390 Evaluate side-chains 87 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain M residue 21 PHE Chi-restraints excluded: chain M residue 31 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 0.0770 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.123171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.106074 restraints weight = 8635.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.108909 restraints weight = 4958.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.110857 restraints weight = 3338.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.112143 restraints weight = 2483.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.113093 restraints weight = 1993.976| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3454 Z= 0.149 Angle : 0.700 8.919 4697 Z= 0.340 Chirality : 0.044 0.167 507 Planarity : 0.004 0.027 600 Dihedral : 5.003 19.830 531 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 4.95 % Allowed : 18.41 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.40), residues: 418 helix: -5.46 (0.27), residues: 6 sheet: 0.33 (0.46), residues: 125 loop : -1.49 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 346 TYR 0.015 0.001 TYR A 453 PHE 0.021 0.002 PHE A 374 TRP 0.008 0.001 TRP A 353 HIS 0.006 0.002 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 3446) covalent geometry : angle 0.69617 / 0.34 ( 4678) SS BOND : bond 0.00413 / 0.29 ( 5) SS BOND : angle 0.82211 / 0.45 ( 10) hydrogen bonds : bond 0.03483 / 2.33 ( 68) hydrogen bonds : angle 6.46940 / 4.23 ( 165) link_BETA1-4 : bond 0.00093 / 0.05 ( 1) link_BETA1-4 : angle 1.15000 / 0.62 ( 3) link_NAG-ASN : bond 0.00186 / 0.09 ( 2) link_NAG-ASN : angle 1.99517 / 1.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.168 Fit side-chains REVERT: A 439 ASN cc_start: 0.6913 (OUTLIER) cc_final: 0.6598 (m-40) REVERT: I 86 ARG cc_start: 0.7885 (mpp80) cc_final: 0.7512 (mpp80) REVERT: I 88 GLU cc_start: 0.7875 (pm20) cc_final: 0.7635 (pm20) REVERT: I 90 THR cc_start: 0.8309 (p) cc_final: 0.7815 (t) REVERT: I 116 THR cc_start: 0.9084 (m) cc_final: 0.8719 (p) REVERT: M 78 LEU cc_start: 0.8081 (mt) cc_final: 0.7780 (mp) outliers start: 18 outliers final: 12 residues processed: 94 average time/residue: 0.0734 time to fit residues: 8.3084 Evaluate side-chains 89 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain M residue 21 PHE Chi-restraints excluded: chain M residue 31 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 2 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.122661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.105576 restraints weight = 8954.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.108517 restraints weight = 5069.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.110431 restraints weight = 3368.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.111762 restraints weight = 2494.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.112653 restraints weight = 1990.126| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3454 Z= 0.163 Angle : 0.750 9.814 4697 Z= 0.366 Chirality : 0.045 0.202 507 Planarity : 0.004 0.031 600 Dihedral : 5.179 22.209 531 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 4.67 % Allowed : 20.05 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.40), residues: 418 helix: -5.46 (0.27), residues: 6 sheet: 0.30 (0.46), residues: 125 loop : -1.56 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 61 TYR 0.016 0.001 TYR A 453 PHE 0.018 0.002 PHE A 374 TRP 0.008 0.001 TRP A 353 HIS 0.006 0.002 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 ( 3446) covalent geometry : angle 0.74596 / 0.37 ( 4678) SS BOND : bond 0.00463 / 0.30 ( 5) SS BOND : angle 0.93065 / 0.43 ( 10) hydrogen bonds : bond 0.03528 / 2.33 ( 68) hydrogen bonds : angle 6.48954 / 4.27 ( 165) link_BETA1-4 : bond 0.00047 / 0.02 ( 1) link_BETA1-4 : angle 1.08684 / 0.59 ( 3) link_NAG-ASN : bond 0.00186 / 0.09 ( 2) link_NAG-ASN : angle 1.99515 / 1.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.108 Fit side-chains REVERT: A 457 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7516 (ttt-90) REVERT: I 80 LEU cc_start: 0.7386 (tt) cc_final: 0.7062 (tt) REVERT: I 86 ARG cc_start: 0.7918 (mpp80) cc_final: 0.7541 (mpp80) REVERT: I 88 GLU cc_start: 0.7816 (pm20) cc_final: 0.7577 (pm20) REVERT: I 90 THR cc_start: 0.8312 (p) cc_final: 0.7798 (t) REVERT: I 116 THR cc_start: 0.9091 (m) cc_final: 0.8728 (p) REVERT: M 78 LEU cc_start: 0.8120 (mt) cc_final: 0.7814 (mp) REVERT: M 81 GLU cc_start: 0.9002 (mp0) cc_final: 0.7852 (tm-30) outliers start: 17 outliers final: 14 residues processed: 84 average time/residue: 0.0643 time to fit residues: 6.6694 Evaluate side-chains 91 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 94 TYR Chi-restraints excluded: chain M residue 21 PHE Chi-restraints excluded: chain M residue 31 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.4980 chunk 36 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 15 optimal weight: 0.1980 chunk 28 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.122966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.105325 restraints weight = 8856.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.108389 restraints weight = 4995.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.110381 restraints weight = 3299.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.111725 restraints weight = 2439.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.112702 restraints weight = 1947.327| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3454 Z= 0.123 Angle : 0.721 10.408 4697 Z= 0.348 Chirality : 0.044 0.190 507 Planarity : 0.004 0.029 600 Dihedral : 4.776 21.064 531 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 3.85 % Allowed : 20.33 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.39), residues: 418 helix: -5.45 (0.27), residues: 6 sheet: 0.30 (0.46), residues: 125 loop : -1.54 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 61 TYR 0.012 0.001 TYR A 453 PHE 0.014 0.002 PHE M 98 TRP 0.009 0.001 TRP A 353 HIS 0.003 0.001 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 ( 3446) covalent geometry : angle 0.71705 / 0.35 ( 4678) SS BOND : bond 0.00379 / 0.24 ( 5) SS BOND : angle 0.83081 / 0.39 ( 10) hydrogen bonds : bond 0.03190 / 2.16 ( 68) hydrogen bonds : angle 6.20909 / 4.09 ( 165) link_BETA1-4 : bond 0.00087 / 0.05 ( 1) link_BETA1-4 : angle 1.48752 / 0.78 ( 3) link_NAG-ASN : bond 0.00130 / 0.06 ( 2) link_NAG-ASN : angle 1.98851 / 1.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.088 Fit side-chains REVERT: I 86 ARG cc_start: 0.7950 (mpp80) cc_final: 0.7560 (mpp80) REVERT: I 88 GLU cc_start: 0.7815 (pm20) cc_final: 0.7566 (pm20) REVERT: I 90 THR cc_start: 0.8332 (p) cc_final: 0.7837 (t) REVERT: I 116 THR cc_start: 0.9117 (m) cc_final: 0.8760 (p) REVERT: M 78 LEU cc_start: 0.8093 (mt) cc_final: 0.7760 (mp) REVERT: M 81 GLU cc_start: 0.8995 (mp0) cc_final: 0.7880 (tm-30) outliers start: 14 outliers final: 12 residues processed: 91 average time/residue: 0.0644 time to fit residues: 7.0685 Evaluate side-chains 89 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain M residue 21 PHE Chi-restraints excluded: chain M residue 31 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 16 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 0.4980 chunk 29 optimal weight: 7.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.119816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.101611 restraints weight = 8695.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.104597 restraints weight = 4793.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.106668 restraints weight = 3164.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.108011 restraints weight = 2319.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.109011 restraints weight = 1849.678| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3454 Z= 0.146 Angle : 0.758 11.339 4697 Z= 0.362 Chirality : 0.044 0.180 507 Planarity : 0.004 0.029 600 Dihedral : 5.095 23.938 531 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 4.40 % Allowed : 20.88 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.39), residues: 418 helix: -5.45 (0.27), residues: 6 sheet: 0.32 (0.49), residues: 112 loop : -1.51 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 457 TYR 0.015 0.001 TYR A 453 PHE 0.019 0.002 PHE A 374 TRP 0.008 0.001 TRP A 436 HIS 0.006 0.001 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 3446) covalent geometry : angle 0.75498 / 0.36 ( 4678) SS BOND : bond 0.00417 / 0.28 ( 5) SS BOND : angle 0.84995 / 0.41 ( 10) hydrogen bonds : bond 0.03268 / 2.18 ( 68) hydrogen bonds : angle 6.15818 / 4.06 ( 165) link_BETA1-4 : bond 0.00185 / 0.10 ( 1) link_BETA1-4 : angle 1.13415 / 0.61 ( 3) link_NAG-ASN : bond 0.00173 / 0.08 ( 2) link_NAG-ASN : angle 1.92298 / 1.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.197 Fit side-chains REVERT: A 406 GLU cc_start: 0.8659 (mp0) cc_final: 0.8448 (pm20) REVERT: I 46 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7890 (mp0) REVERT: I 78 LEU cc_start: 0.8066 (mm) cc_final: 0.7850 (mm) REVERT: I 86 ARG cc_start: 0.7999 (mpp80) cc_final: 0.7597 (mpp80) REVERT: I 88 GLU cc_start: 0.7860 (pm20) cc_final: 0.7592 (pm20) REVERT: I 90 THR cc_start: 0.8366 (p) cc_final: 0.7853 (t) REVERT: I 116 THR cc_start: 0.9138 (m) cc_final: 0.8787 (p) REVERT: M 78 LEU cc_start: 0.8053 (mt) cc_final: 0.7718 (mp) REVERT: M 81 GLU cc_start: 0.9031 (mp0) cc_final: 0.7957 (tm-30) outliers start: 16 outliers final: 14 residues processed: 91 average time/residue: 0.0585 time to fit residues: 6.6269 Evaluate side-chains 94 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 94 TYR Chi-restraints excluded: chain M residue 21 PHE Chi-restraints excluded: chain M residue 31 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 18 optimal weight: 0.0040 chunk 15 optimal weight: 0.0470 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 0.2980 chunk 31 optimal weight: 0.0270 chunk 28 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 0.2980 overall best weight: 0.1348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.124778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.106700 restraints weight = 8829.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.109758 restraints weight = 4960.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.111842 restraints weight = 3275.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.113215 restraints weight = 2402.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.114261 restraints weight = 1919.100| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3454 Z= 0.119 Angle : 0.756 11.300 4697 Z= 0.354 Chirality : 0.045 0.229 507 Planarity : 0.004 0.032 600 Dihedral : 4.405 18.306 531 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 3.57 % Allowed : 21.70 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.40), residues: 418 helix: -5.45 (0.27), residues: 6 sheet: 0.35 (0.46), residues: 123 loop : -1.52 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 61 TYR 0.007 0.001 TYR A 365 PHE 0.010 0.001 PHE I 27 TRP 0.014 0.001 TRP M 35 HIS 0.001 0.000 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 3446) covalent geometry : angle 0.75155 / 0.35 ( 4678) SS BOND : bond 0.00175 / 0.12 ( 5) SS BOND : angle 0.71185 / 0.34 ( 10) hydrogen bonds : bond 0.02987 / 2.00 ( 68) hydrogen bonds : angle 6.03381 / 3.99 ( 165) link_BETA1-4 : bond 0.00333 / 0.18 ( 1) link_BETA1-4 : angle 2.11898 / 1.08 ( 3) link_NAG-ASN : bond 0.00233 / 0.12 ( 2) link_NAG-ASN : angle 1.90697 / 1.09 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.081 Fit side-chains revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8553 (mp0) cc_final: 0.8350 (pm20) REVERT: I 82 MET cc_start: 0.8367 (mmm) cc_final: 0.7947 (mmm) REVERT: I 88 GLU cc_start: 0.7650 (pm20) cc_final: 0.7294 (pm20) REVERT: I 90 THR cc_start: 0.8307 (p) cc_final: 0.7847 (t) REVERT: I 116 THR cc_start: 0.9141 (m) cc_final: 0.8733 (p) REVERT: M 78 LEU cc_start: 0.8039 (mt) cc_final: 0.7688 (mp) REVERT: M 81 GLU cc_start: 0.9007 (mp0) cc_final: 0.7959 (tm-30) outliers start: 13 outliers final: 11 residues processed: 92 average time/residue: 0.0563 time to fit residues: 6.4314 Evaluate side-chains 91 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain M residue 21 PHE Chi-restraints excluded: chain M residue 31 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 27 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.122564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.104819 restraints weight = 9044.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.107831 restraints weight = 5145.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.109784 restraints weight = 3404.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.111164 restraints weight = 2520.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.112099 restraints weight = 2007.633| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3454 Z= 0.146 Angle : 0.819 12.135 4697 Z= 0.385 Chirality : 0.045 0.210 507 Planarity : 0.004 0.031 600 Dihedral : 4.989 21.774 531 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 3.02 % Allowed : 23.35 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.40), residues: 418 helix: -5.45 (0.27), residues: 6 sheet: 0.39 (0.46), residues: 125 loop : -1.49 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 61 TYR 0.014 0.001 TYR A 453 PHE 0.020 0.002 PHE A 374 TRP 0.006 0.001 TRP A 436 HIS 0.006 0.001 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 3446) covalent geometry : angle 0.81642 / 0.38 ( 4678) SS BOND : bond 0.00328 / 0.22 ( 5) SS BOND : angle 0.75837 / 0.35 ( 10) hydrogen bonds : bond 0.03169 / 2.13 ( 68) hydrogen bonds : angle 6.04826 / 4.02 ( 165) link_BETA1-4 : bond 0.00075 / 0.04 ( 1) link_BETA1-4 : angle 1.14759 / 0.61 ( 3) link_NAG-ASN : bond 0.00182 / 0.09 ( 2) link_NAG-ASN : angle 1.83937 / 1.04 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 795.40 seconds wall clock time: 14 minutes 25.31 seconds (865.31 seconds total)