Starting phenix.real_space_refine on Thu Mar 6 06:35:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y0w_33552/03_2025/7y0w_33552_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y0w_33552/03_2025/7y0w_33552.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y0w_33552/03_2025/7y0w_33552.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y0w_33552/03_2025/7y0w_33552.map" model { file = "/net/cci-nas-00/data/ceres_data/7y0w_33552/03_2025/7y0w_33552_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y0w_33552/03_2025/7y0w_33552_neut.cif" } resolution = 3.42 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= 0.023 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 22 5.16 5 C 3222 2.51 5 N 853 2.21 5 O 989 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5086 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 930 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 6, 'TRANS': 116} Chain: "B" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 826 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 927 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 817 Classifications: {'peptide': 109} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "R" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1548 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 181} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "X" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.04, per 1000 atoms: 0.79 Number of scatterers: 5086 At special positions: 0 Unit cell: (102.96, 91.52, 83.2, 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 22 16.00 O 989 8.00 N 853 7.00 C 3222 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.06 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " 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 X 1 " - " NAG X 2 " BETA1-6 " NAG X 1 " - " FUC X 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 583.9 milliseconds 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1188 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 13 sheets defined 5.7% alpha, 32.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.991A pdb=" N ILE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.789A pdb=" N ASP H 90 " --> pdb=" O LYS H 87 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'L' and resid 81 through 85 removed outlier: 3.525A pdb=" N ASP L 84 " --> pdb=" O GLN L 81 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER L 85 " --> pdb=" O SER L 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 81 through 85' Processing helix chain 'R' and resid 349 through 353 removed outlier: 3.533A pdb=" N TRP R 353 " --> pdb=" O VAL R 350 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 371 removed outlier: 3.966A pdb=" N VAL R 367 " --> pdb=" O ASP R 364 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU R 368 " --> pdb=" O TYR R 365 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TYR R 369 " --> pdb=" O SER R 366 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASN R 370 " --> pdb=" O VAL R 367 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU R 371 " --> pdb=" O LEU R 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 364 through 371' Processing helix chain 'R' and resid 405 through 407 No H-bonds generated for 'chain 'R' and resid 405 through 407' Processing helix chain 'R' and resid 417 through 422 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.568A pdb=" N GLU A 10 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY A 49 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.568A pdb=" N GLU A 10 " --> pdb=" O THR A 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 5 through 7 removed outlier: 3.553A pdb=" N CYS B 23 " --> pdb=" O PHE B 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12 Processing sheet with id=AA6, first strand: chain 'B' and resid 45 through 48 removed outlier: 5.559A pdb=" N LEU B 46 " --> pdb=" O GLN B 37 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLN B 37 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.239A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N CYS H 96 " --> pdb=" O GLY H 111 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.239A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.505A pdb=" N PHE L 73 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU L 72 " --> pdb=" O SER L 69 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER L 65 " --> pdb=" O THR L 76 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.156A pdb=" N LEU L 11 " --> pdb=" O GLU L 107 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR L 88 " --> pdb=" O THR L 104 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU L 35 " --> pdb=" O TYR L 51 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N TYR L 51 " --> pdb=" O LEU L 35 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 354 through 358 Processing sheet with id=AB3, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AB4, first strand: chain 'R' and resid 473 through 474 153 hydrogen bonds defined for protein. 372 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: 1.37 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 1635 1.35 - 1.48: 1497 1.48 - 1.62: 2055 1.62 - 1.76: 0 1.76 - 1.89: 28 Bond restraints: 5215 Sorted by residual: bond pdb=" CB CYS R 432 " pdb=" SG CYS R 432 " ideal model delta sigma weight residual 1.808 1.890 -0.082 3.30e-02 9.18e+02 6.24e+00 bond pdb=" CB LYS H 87 " pdb=" CG LYS H 87 " ideal model delta sigma weight residual 1.520 1.573 -0.053 3.00e-02 1.11e+03 3.12e+00 bond pdb=" CG LYS H 87 " pdb=" CD LYS H 87 " ideal model delta sigma weight residual 1.520 1.571 -0.051 3.00e-02 1.11e+03 2.85e+00 bond pdb=" CA ASP H 54 " pdb=" CB ASP H 54 " ideal model delta sigma weight residual 1.533 1.561 -0.028 1.66e-02 3.63e+03 2.82e+00 bond pdb=" CB GLN A 62 " pdb=" CG GLN A 62 " ideal model delta sigma weight residual 1.520 1.569 -0.049 3.00e-02 1.11e+03 2.70e+00 ... (remaining 5210 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.04: 6966 3.04 - 6.08: 104 6.08 - 9.12: 15 9.12 - 12.15: 2 12.15 - 15.19: 2 Bond angle restraints: 7089 Sorted by residual: angle pdb=" CA CYS R 379 " pdb=" CB CYS R 379 " pdb=" SG CYS R 379 " ideal model delta sigma weight residual 114.40 129.59 -15.19 2.30e+00 1.89e-01 4.36e+01 angle pdb=" N CYS R 361 " pdb=" CA CYS R 361 " pdb=" C CYS R 361 " ideal model delta sigma weight residual 109.18 116.62 -7.44 1.42e+00 4.96e-01 2.74e+01 angle pdb=" CB LYS H 87 " pdb=" CG LYS H 87 " pdb=" CD LYS H 87 " ideal model delta sigma weight residual 111.30 123.07 -11.77 2.30e+00 1.89e-01 2.62e+01 angle pdb=" N CYS R 379 " pdb=" CA CYS R 379 " pdb=" C CYS R 379 " ideal model delta sigma weight residual 108.96 115.12 -6.16 1.49e+00 4.50e-01 1.71e+01 angle pdb=" C SER L 32 " pdb=" N THR L 33 " pdb=" CA THR L 33 " ideal model delta sigma weight residual 122.07 127.98 -5.91 1.43e+00 4.89e-01 1.71e+01 ... (remaining 7084 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 2761 17.38 - 34.76: 271 34.76 - 52.13: 49 52.13 - 69.51: 8 69.51 - 86.89: 8 Dihedral angle restraints: 3097 sinusoidal: 1227 harmonic: 1870 Sorted by residual: dihedral pdb=" CB CYS R 391 " pdb=" SG CYS R 391 " pdb=" SG CYS R 525 " pdb=" CB CYS R 525 " ideal model delta sinusoidal sigma weight residual 93.00 14.17 78.83 1 1.00e+01 1.00e-02 7.74e+01 dihedral pdb=" CA LEU A 99 " pdb=" C LEU A 99 " pdb=" N PHE A 100 " pdb=" CA PHE A 100 " ideal model delta harmonic sigma weight residual 180.00 -141.97 -38.03 0 5.00e+00 4.00e-02 5.78e+01 dihedral pdb=" CA CYS R 361 " pdb=" C CYS R 361 " pdb=" N VAL R 362 " pdb=" CA VAL R 362 " ideal model delta harmonic sigma weight residual 180.00 146.38 33.62 0 5.00e+00 4.00e-02 4.52e+01 ... (remaining 3094 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 694 0.098 - 0.196: 66 0.196 - 0.294: 9 0.294 - 0.393: 2 0.393 - 0.491: 1 Chirality restraints: 772 Sorted by residual: chirality pdb=" C1 FUC X 3 " pdb=" O6 NAG X 1 " pdb=" C2 FUC X 3 " pdb=" O5 FUC X 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 8.53e+00 chirality pdb=" CB ILE H 34 " pdb=" CA ILE H 34 " pdb=" CG1 ILE H 34 " pdb=" CG2 ILE H 34 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.49 2.00e-01 2.50e+01 6.02e+00 chirality pdb=" CB ILE H 51 " pdb=" CA ILE H 51 " pdb=" CG1 ILE H 51 " pdb=" CG2 ILE H 51 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 769 not shown) Planarity restraints: 915 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG X 1 " 0.107 2.00e-02 2.50e+03 8.85e-02 9.78e+01 pdb=" C7 NAG X 1 " -0.028 2.00e-02 2.50e+03 pdb=" C8 NAG X 1 " 0.081 2.00e-02 2.50e+03 pdb=" N2 NAG X 1 " -0.141 2.00e-02 2.50e+03 pdb=" O7 NAG X 1 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG X 2 " -0.059 2.00e-02 2.50e+03 4.85e-02 2.94e+01 pdb=" C7 NAG X 2 " 0.019 2.00e-02 2.50e+03 pdb=" C8 NAG X 2 " -0.046 2.00e-02 2.50e+03 pdb=" N2 NAG X 2 " 0.076 2.00e-02 2.50e+03 pdb=" O7 NAG X 2 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 107 " -0.049 5.00e-02 4.00e+02 7.50e-02 9.00e+00 pdb=" N PRO A 108 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 108 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 108 " -0.042 5.00e-02 4.00e+02 ... (remaining 912 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 1538 2.82 - 3.34: 3997 3.34 - 3.86: 8403 3.86 - 4.38: 9574 4.38 - 4.90: 17257 Nonbonded interactions: 40769 Sorted by model distance: nonbonded pdb=" OG SER R 469 " pdb=" OE1 GLU R 471 " model vdw 2.295 3.040 nonbonded pdb=" O GLY H 8 " pdb=" OG1 THR H 114 " model vdw 2.332 3.040 nonbonded pdb=" OE2 GLU R 406 " pdb=" OH TYR R 495 " model vdw 2.338 3.040 nonbonded pdb=" O ASN R 439 " pdb=" OG SER R 443 " model vdw 2.353 3.040 nonbonded pdb=" O SER A 107 " pdb=" OG SER A 107 " model vdw 2.359 3.040 ... (remaining 40764 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: 6.940 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: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.340 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 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 0.082 5215 Z= 0.400 Angle : 0.954 15.192 7089 Z= 0.514 Chirality : 0.062 0.491 772 Planarity : 0.008 0.088 915 Dihedral : 14.239 86.888 1888 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 0.18 % Allowed : 0.55 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -2.40 (0.32), residues: 641 helix: -4.93 (0.34), residues: 22 sheet: -1.28 (0.32), residues: 284 loop : -1.57 (0.30), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 36 HIS 0.006 0.002 HIS H 35 PHE 0.020 0.002 PHE R 347 TYR 0.030 0.002 TYR R 380 ARG 0.015 0.001 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.583 Fit side-chains REVERT: R 378 LYS cc_start: 0.7896 (ptpp) cc_final: 0.7673 (pttm) REVERT: R 390 LEU cc_start: 0.8148 (tp) cc_final: 0.7756 (tp) outliers start: 1 outliers final: 0 residues processed: 109 average time/residue: 0.1709 time to fit residues: 25.0419 Evaluate side-chains 92 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN H 62 GLN H 112 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.124927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.100932 restraints weight = 6737.124| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.01 r_work: 0.2930 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5215 Z= 0.277 Angle : 0.629 7.314 7089 Z= 0.337 Chirality : 0.048 0.238 772 Planarity : 0.005 0.062 915 Dihedral : 5.378 28.883 773 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.28 % Allowed : 11.54 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % 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: -2.14 (0.32), residues: 641 helix: -4.91 (0.37), residues: 22 sheet: -1.09 (0.31), residues: 288 loop : -1.39 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 96 HIS 0.004 0.001 HIS H 35 PHE 0.011 0.001 PHE B 73 TYR 0.017 0.001 TYR L 93 ARG 0.004 0.000 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.630 Fit side-chains REVERT: R 390 LEU cc_start: 0.8357 (tp) cc_final: 0.8148 (tp) outliers start: 7 outliers final: 6 residues processed: 96 average time/residue: 0.1736 time to fit residues: 22.1798 Evaluate side-chains 94 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain R residue 336 CYS Chi-restraints excluded: chain R residue 349 SER Chi-restraints excluded: chain R residue 392 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 50 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 35 optimal weight: 0.0970 chunk 55 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.3388 r_free = 0.3388 target = 0.125081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.101459 restraints weight = 6735.385| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.98 r_work: 0.2947 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5215 Z= 0.222 Angle : 0.569 6.558 7089 Z= 0.303 Chirality : 0.046 0.185 772 Planarity : 0.004 0.056 915 Dihedral : 4.940 29.870 773 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.20 % Allowed : 15.75 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.33), residues: 641 helix: -4.98 (0.29), residues: 28 sheet: -0.86 (0.31), residues: 288 loop : -1.31 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 96 HIS 0.003 0.001 HIS H 27 PHE 0.010 0.001 PHE R 490 TYR 0.014 0.001 TYR L 93 ARG 0.006 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.578 Fit side-chains REVERT: A 110 ASP cc_start: 0.6605 (m-30) cc_final: 0.6346 (m-30) REVERT: H 87 LYS cc_start: 0.8074 (mmmt) cc_final: 0.7748 (tppt) REVERT: R 390 LEU cc_start: 0.8357 (tp) cc_final: 0.8145 (tp) outliers start: 12 outliers final: 8 residues processed: 101 average time/residue: 0.1371 time to fit residues: 19.0012 Evaluate side-chains 96 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain R residue 336 CYS Chi-restraints excluded: chain R residue 349 SER Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 392 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 0.0570 chunk 40 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 487 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.123245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.099338 restraints weight = 6908.653| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.01 r_work: 0.2917 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5215 Z= 0.272 Angle : 0.574 6.415 7089 Z= 0.306 Chirality : 0.047 0.205 772 Planarity : 0.004 0.055 915 Dihedral : 4.874 28.697 773 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 2.93 % Allowed : 17.58 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.33), residues: 641 helix: -4.96 (0.28), residues: 28 sheet: -0.80 (0.31), residues: 291 loop : -1.31 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 96 HIS 0.004 0.001 HIS H 35 PHE 0.010 0.001 PHE A 100 TYR 0.016 0.001 TYR L 93 ARG 0.004 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.612 Fit side-chains REVERT: A 110 ASP cc_start: 0.6727 (m-30) cc_final: 0.6415 (m-30) REVERT: B 70 ASP cc_start: 0.8366 (m-30) cc_final: 0.8160 (m-30) REVERT: H 81 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8874 (tp) REVERT: H 87 LYS cc_start: 0.8127 (mmmt) cc_final: 0.7763 (tppt) outliers start: 16 outliers final: 10 residues processed: 100 average time/residue: 0.1661 time to fit residues: 22.4472 Evaluate side-chains 100 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain R residue 336 CYS Chi-restraints excluded: chain R residue 349 SER Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 392 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 1 optimal weight: 0.8980 chunk 31 optimal weight: 0.4980 chunk 54 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3360 r_free = 0.3360 target = 0.123095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.098904 restraints weight = 6849.442| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.04 r_work: 0.2909 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5215 Z= 0.281 Angle : 0.575 6.532 7089 Z= 0.304 Chirality : 0.047 0.205 772 Planarity : 0.004 0.054 915 Dihedral : 4.843 29.426 773 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 3.11 % Allowed : 18.68 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.33), residues: 641 helix: -5.05 (0.22), residues: 28 sheet: -0.75 (0.31), residues: 291 loop : -1.37 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 96 HIS 0.003 0.001 HIS H 27 PHE 0.010 0.001 PHE A 100 TYR 0.016 0.001 TYR L 93 ARG 0.006 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.565 Fit side-chains REVERT: A 110 ASP cc_start: 0.6795 (m-30) cc_final: 0.6573 (m-30) REVERT: H 87 LYS cc_start: 0.8138 (mmmt) cc_final: 0.7753 (tppt) REVERT: H 112 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8551 (pt0) outliers start: 17 outliers final: 12 residues processed: 101 average time/residue: 0.2017 time to fit residues: 27.5797 Evaluate side-chains 101 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain R residue 336 CYS Chi-restraints excluded: chain R residue 349 SER Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 392 PHE Chi-restraints excluded: chain R residue 468 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3340 r_free = 0.3340 target = 0.121658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.097432 restraints weight = 6896.100| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.03 r_work: 0.2890 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5215 Z= 0.325 Angle : 0.594 6.707 7089 Z= 0.314 Chirality : 0.047 0.195 772 Planarity : 0.004 0.056 915 Dihedral : 4.899 28.995 773 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 3.85 % Allowed : 18.13 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.33), residues: 641 helix: -4.99 (0.26), residues: 28 sheet: -0.79 (0.31), residues: 291 loop : -1.39 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 96 HIS 0.003 0.001 HIS H 35 PHE 0.011 0.001 PHE A 100 TYR 0.018 0.002 TYR L 93 ARG 0.004 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.621 Fit side-chains REVERT: A 110 ASP cc_start: 0.6840 (m-30) cc_final: 0.6623 (m-30) REVERT: B 106 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7320 (mm-30) REVERT: H 99 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8128 (mt-10) REVERT: H 112 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8572 (pt0) REVERT: R 383 SER cc_start: 0.8839 (t) cc_final: 0.8600 (p) outliers start: 21 outliers final: 15 residues processed: 100 average time/residue: 0.1449 time to fit residues: 19.3673 Evaluate side-chains 104 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain R residue 336 CYS Chi-restraints excluded: chain R residue 349 SER Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 390 LEU Chi-restraints excluded: chain R residue 391 CYS Chi-restraints excluded: chain R residue 392 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3359 r_free = 0.3359 target = 0.122892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.098931 restraints weight = 6772.751| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.01 r_work: 0.2911 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5215 Z= 0.262 Angle : 0.576 6.565 7089 Z= 0.303 Chirality : 0.047 0.238 772 Planarity : 0.004 0.052 915 Dihedral : 4.813 29.042 773 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.75 % Allowed : 19.60 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.33), residues: 641 helix: -4.94 (0.26), residues: 29 sheet: -0.76 (0.31), residues: 291 loop : -1.32 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 96 HIS 0.003 0.001 HIS H 35 PHE 0.011 0.001 PHE A 100 TYR 0.016 0.001 TYR L 93 ARG 0.004 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.476 Fit side-chains REVERT: H 112 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8506 (pt0) REVERT: R 383 SER cc_start: 0.8845 (t) cc_final: 0.8500 (p) outliers start: 15 outliers final: 13 residues processed: 96 average time/residue: 0.1490 time to fit residues: 19.3654 Evaluate side-chains 101 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain R residue 336 CYS Chi-restraints excluded: chain R residue 349 SER Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 390 LEU Chi-restraints excluded: chain R residue 392 PHE Chi-restraints excluded: chain R residue 468 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 3 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 11 optimal weight: 0.0770 chunk 54 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 51 optimal weight: 0.3980 chunk 32 optimal weight: 0.7980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 95 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 = 0.3374 r_free = 0.3374 target = 0.123955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.100157 restraints weight = 6780.252| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.98 r_work: 0.2929 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5215 Z= 0.239 Angle : 0.563 6.505 7089 Z= 0.297 Chirality : 0.046 0.207 772 Planarity : 0.004 0.054 915 Dihedral : 4.710 28.291 773 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 3.85 % Allowed : 19.05 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.33), residues: 641 helix: -4.98 (0.26), residues: 28 sheet: -0.71 (0.31), residues: 290 loop : -1.28 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 96 HIS 0.003 0.001 HIS H 35 PHE 0.010 0.001 PHE A 100 TYR 0.015 0.001 TYR L 93 ARG 0.007 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.542 Fit side-chains REVERT: A 110 ASP cc_start: 0.6657 (m-30) cc_final: 0.6348 (m-30) REVERT: H 112 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8474 (pt0) REVERT: R 383 SER cc_start: 0.8841 (t) cc_final: 0.8506 (p) outliers start: 21 outliers final: 15 residues processed: 100 average time/residue: 0.1418 time to fit residues: 19.2671 Evaluate side-chains 101 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain R residue 336 CYS Chi-restraints excluded: chain R residue 349 SER Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 391 CYS Chi-restraints excluded: chain R residue 392 PHE Chi-restraints excluded: chain R residue 468 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 20 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 39 optimal weight: 0.0870 chunk 16 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.124053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.100181 restraints weight = 6775.841| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.01 r_work: 0.2934 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5215 Z= 0.234 Angle : 0.569 6.930 7089 Z= 0.303 Chirality : 0.046 0.214 772 Planarity : 0.004 0.052 915 Dihedral : 4.674 28.127 773 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 2.93 % Allowed : 20.88 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.33), residues: 641 helix: -4.95 (0.32), residues: 22 sheet: -0.72 (0.31), residues: 292 loop : -1.16 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 96 HIS 0.003 0.001 HIS H 35 PHE 0.010 0.001 PHE A 100 TYR 0.015 0.001 TYR L 93 ARG 0.007 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.578 Fit side-chains REVERT: A 110 ASP cc_start: 0.6621 (m-30) cc_final: 0.6334 (m-30) REVERT: H 112 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8491 (pt0) REVERT: R 383 SER cc_start: 0.8842 (t) cc_final: 0.8502 (p) outliers start: 16 outliers final: 13 residues processed: 95 average time/residue: 0.1371 time to fit residues: 18.0146 Evaluate side-chains 96 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain R residue 336 CYS Chi-restraints excluded: chain R residue 349 SER Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 391 CYS Chi-restraints excluded: chain R residue 392 PHE Chi-restraints excluded: chain R residue 468 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 59 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 95 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 = 0.3369 r_free = 0.3369 target = 0.123571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.099760 restraints weight = 6730.536| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.99 r_work: 0.2923 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5215 Z= 0.254 Angle : 0.572 6.458 7089 Z= 0.301 Chirality : 0.047 0.209 772 Planarity : 0.004 0.053 915 Dihedral : 4.664 27.900 773 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.30 % Allowed : 20.51 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.33), residues: 641 helix: -4.93 (0.34), residues: 22 sheet: -0.71 (0.31), residues: 292 loop : -1.18 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 96 HIS 0.003 0.001 HIS H 35 PHE 0.010 0.001 PHE A 100 TYR 0.016 0.001 TYR L 93 ARG 0.007 0.000 ARG L 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.580 Fit side-chains REVERT: A 110 ASP cc_start: 0.6735 (m-30) cc_final: 0.6430 (m-30) REVERT: H 112 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8522 (pt0) REVERT: R 383 SER cc_start: 0.8826 (t) cc_final: 0.8494 (p) outliers start: 18 outliers final: 15 residues processed: 90 average time/residue: 0.1424 time to fit residues: 17.5855 Evaluate side-chains 97 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain R residue 336 CYS Chi-restraints excluded: chain R residue 349 SER Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 391 CYS Chi-restraints excluded: chain R residue 392 PHE Chi-restraints excluded: chain R residue 468 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 8 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 54 optimal weight: 0.0010 chunk 31 optimal weight: 0.9980 chunk 53 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 43 GLN ** L 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.124812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.100850 restraints weight = 6834.092| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.02 r_work: 0.2944 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5215 Z= 0.218 Angle : 0.553 6.395 7089 Z= 0.290 Chirality : 0.046 0.202 772 Planarity : 0.004 0.052 915 Dihedral : 4.578 27.563 773 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.93 % Allowed : 20.88 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.33), residues: 641 helix: -4.94 (0.33), residues: 22 sheet: -0.69 (0.31), residues: 289 loop : -1.17 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 96 HIS 0.003 0.001 HIS H 35 PHE 0.009 0.001 PHE A 100 TYR 0.014 0.001 TYR L 93 ARG 0.007 0.000 ARG L 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3449.65 seconds wall clock time: 61 minutes 17.66 seconds (3677.66 seconds total)