Starting phenix.real_space_refine on Tue Jan 14 02:34:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y0w_33552/01_2025/7y0w_33552_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y0w_33552/01_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_33552/01_2025/7y0w_33552.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y0w_33552/01_2025/7y0w_33552.map" model { file = "/net/cci-nas-00/data/ceres_data/7y0w_33552/01_2025/7y0w_33552_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y0w_33552/01_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-5571/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: 4.13, per 1000 atoms: 0.81 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: 1.40 Conformation dependent library (CDL) restraints added in 763.9 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: 0.65 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: 1.52 Time building geometry restraints manager: 1.42 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: 2.630 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.380 Find NCS groups from input model: 0.060 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.320 ------------------------------------------------------------------------------- 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 : 0.613 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: 0.1569 time to fit residues: 22.7214 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 : 0.570 ------------------------------------------------------------------------------- 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 = 49)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.100931 restraints weight = 6737.127| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.01 r_work: 0.2930 rms_B_bonded: 2.62 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: 0.8259 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 : 0.568 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: 0.1648 time to fit residues: 20.9841 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 : 0.559 ------------------------------------------------------------------------------- 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: 0.9990 chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 61 optimal weight: 0.0060 chunk 35 optimal weight: 0.0870 chunk 55 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.4774 ------------------------------------------------------------------------------- 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 = 0.3400 r_free = 0.3400 target = 0.126112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.102511 restraints weight = 6720.088| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.99 r_work: 0.2978 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1670 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= 0.197 Angle : 0.556 6.443 7089 Z= 0.297 Chirality : 0.046 0.178 772 Planarity : 0.004 0.056 915 Dihedral : 4.862 29.474 773 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.83 % Allowed : 15.57 % Favored : 82.60 % 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: -4.99 (0.28), residues: 28 sheet: -0.86 (0.31), residues: 289 loop : -1.26 (0.34), residues: 324 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 0.011 0.001 PHE R 490 TYR 0.014 0.001 TYR R 369 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 103 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.460 Fit side-chains REVERT: A 110 ASP cc_start: 0.6722 (m-30) cc_final: 0.6479 (m-30) REVERT: H 87 LYS cc_start: 0.8056 (mmmt) cc_final: 0.7724 (tppt) REVERT: R 390 LEU cc_start: 0.8351 (tp) cc_final: 0.8146 (tp) outliers start: 10 outliers final: 7 residues processed: 100 average time/residue: 0.1480 time to fit residues: 20.0763 Evaluate side-chains 94 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 36 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 27 HIS R 487 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.115786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.092674 restraints weight = 7153.727| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.91 r_work: 0.2817 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.065 5215 Z= 0.722 Angle : 0.787 8.485 7089 Z= 0.418 Chirality : 0.055 0.287 772 Planarity : 0.006 0.069 915 Dihedral : 5.713 31.511 773 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % 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 : 0.33 % 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: -2.28 (0.33), residues: 641 helix: -4.64 (0.46), residues: 29 sheet: -1.03 (0.32), residues: 291 loop : -1.59 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP H 50 HIS 0.007 0.002 HIS H 35 PHE 0.017 0.002 PHE B 73 TYR 0.027 0.003 TYR L 93 ARG 0.006 0.001 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 110 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.597 Fit side-chains REVERT: A 110 ASP cc_start: 0.7109 (m-30) cc_final: 0.6899 (m-30) REVERT: H 87 LYS cc_start: 0.8138 (mmmt) cc_final: 0.7765 (tppt) REVERT: L 104 THR cc_start: 0.9150 (m) cc_final: 0.8887 (p) outliers start: 16 outliers final: 12 residues processed: 102 average time/residue: 0.1695 time to fit residues: 22.6873 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 : 0.519 ------------------------------------------------------------------------------- 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 20 THR 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 392 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 1 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 47 optimal weight: 0.4980 chunk 5 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3342 r_free = 0.3342 target = 0.121705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.097602 restraints weight = 6870.778| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.02 r_work: 0.2888 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5215 Z= 0.249 Angle : 0.584 6.936 7089 Z= 0.311 Chirality : 0.047 0.184 772 Planarity : 0.004 0.051 915 Dihedral : 5.078 30.549 773 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.85 % Allowed : 18.50 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.13 (0.33), residues: 641 helix: -4.85 (0.31), residues: 29 sheet: -0.93 (0.31), residues: 291 loop : -1.47 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 96 HIS 0.004 0.001 HIS H 35 PHE 0.013 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 116 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.610 Fit side-chains REVERT: H 81 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8885 (tp) REVERT: L 18 ARG cc_start: 0.8192 (mmm-85) cc_final: 0.7953 (mmm-85) outliers start: 21 outliers final: 14 residues processed: 108 average time/residue: 0.1809 time to fit residues: 25.5960 Evaluate side-chains 108 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 46 GLU 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 44 GLN 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 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: 3.9990 chunk 21 optimal weight: 0.0970 chunk 53 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 17 optimal weight: 0.0040 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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 = 0.3362 r_free = 0.3362 target = 0.123341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.099239 restraints weight = 6843.339| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.01 r_work: 0.2914 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 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 : 0.003 0.042 5215 Z= 0.222 Angle : 0.562 6.315 7089 Z= 0.299 Chirality : 0.046 0.200 772 Planarity : 0.004 0.057 915 Dihedral : 4.811 28.090 773 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 4.21 % Allowed : 19.05 % Favored : 76.74 % 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: -2.01 (0.33), residues: 641 helix: -4.88 (0.30), residues: 29 sheet: -0.82 (0.31), residues: 290 loop : -1.40 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 96 HIS 0.002 0.001 HIS H 35 PHE 0.011 0.001 PHE A 100 TYR 0.018 0.001 TYR A 80 ARG 0.006 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 114 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.526 Fit side-chains REVERT: A 110 ASP cc_start: 0.6723 (m-30) cc_final: 0.6421 (m-30) REVERT: B 106 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7405 (mm-30) REVERT: H 112 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8518 (pt0) REVERT: L 18 ARG cc_start: 0.8122 (mmm-85) cc_final: 0.7894 (mmm-85) REVERT: R 383 SER cc_start: 0.8837 (t) cc_final: 0.8630 (p) outliers start: 23 outliers final: 14 residues processed: 105 average time/residue: 0.1548 time to fit residues: 21.8709 Evaluate side-chains 106 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 13 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 50 optimal weight: 0.0000 chunk 53 optimal weight: 1.9990 chunk 19 optimal weight: 0.0980 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 38 optimal weight: 0.3980 chunk 26 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 overall best weight: 0.3784 ------------------------------------------------------------------------------- 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 = 0.3396 r_free = 0.3396 target = 0.125661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.102112 restraints weight = 6715.303| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.97 r_work: 0.2949 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5215 Z= 0.184 Angle : 0.541 6.173 7089 Z= 0.287 Chirality : 0.046 0.217 772 Planarity : 0.004 0.052 915 Dihedral : 4.629 28.044 773 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.30 % Allowed : 20.33 % Favored : 76.37 % 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: -1.82 (0.34), residues: 641 helix: -4.94 (0.29), residues: 28 sheet: -0.73 (0.32), residues: 290 loop : -1.21 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 96 HIS 0.002 0.001 HIS H 35 PHE 0.009 0.001 PHE A 100 TYR 0.013 0.001 TYR L 93 ARG 0.006 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 108 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.533 Fit side-chains REVERT: A 110 ASP cc_start: 0.6692 (m-30) cc_final: 0.6380 (m-30) REVERT: H 13 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7918 (mtmt) REVERT: H 112 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8496 (pt0) REVERT: L 18 ARG cc_start: 0.8143 (mmm-85) cc_final: 0.7922 (mmm-85) outliers start: 18 outliers final: 13 residues processed: 102 average time/residue: 0.1625 time to fit residues: 22.2752 Evaluate side-chains 99 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 13 LYS 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 55 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.1959 > 50: distance: 72 - 76: 18.052 distance: 76 - 77: 21.869 distance: 77 - 78: 33.446 distance: 77 - 80: 28.291 distance: 78 - 85: 21.940 distance: 80 - 81: 30.315 distance: 81 - 82: 27.707 distance: 82 - 83: 21.217 distance: 83 - 84: 12.338 distance: 85 - 86: 24.343 distance: 86 - 87: 9.697 distance: 86 - 89: 36.702 distance: 87 - 88: 8.886 distance: 87 - 92: 3.615 distance: 89 - 90: 9.987 distance: 89 - 91: 17.528 distance: 92 - 93: 6.045 distance: 93 - 94: 16.582 distance: 93 - 96: 23.435 distance: 94 - 95: 16.392 distance: 94 - 98: 39.975 distance: 96 - 97: 19.147 distance: 98 - 99: 4.452 distance: 99 - 100: 15.344 distance: 100 - 101: 31.606 distance: 100 - 102: 10.861 distance: 102 - 103: 25.762 distance: 103 - 104: 31.633 distance: 103 - 106: 22.443 distance: 104 - 105: 14.466 distance: 104 - 110: 14.586 distance: 106 - 107: 18.797 distance: 107 - 108: 12.209 distance: 107 - 109: 23.204 distance: 110 - 111: 11.636 distance: 111 - 112: 8.233 distance: 111 - 114: 9.548 distance: 112 - 113: 9.004 distance: 112 - 122: 7.425 distance: 114 - 115: 11.437 distance: 115 - 116: 22.761 distance: 115 - 117: 11.134 distance: 116 - 118: 22.948 distance: 117 - 119: 18.967 distance: 118 - 120: 3.670 distance: 119 - 120: 12.176 distance: 120 - 121: 18.391 distance: 122 - 123: 8.977 distance: 123 - 124: 10.479 distance: 123 - 126: 20.360 distance: 124 - 125: 17.722 distance: 124 - 130: 10.491 distance: 126 - 127: 14.915 distance: 127 - 128: 14.450 distance: 127 - 129: 23.494 distance: 130 - 131: 5.528 distance: 131 - 132: 14.566 distance: 131 - 134: 13.359 distance: 132 - 133: 26.074 distance: 132 - 142: 8.384 distance: 134 - 135: 10.950 distance: 135 - 136: 19.592 distance: 135 - 137: 10.809 distance: 136 - 138: 14.589 distance: 137 - 139: 12.703 distance: 138 - 140: 12.545 distance: 139 - 140: 10.147 distance: 140 - 141: 22.602 distance: 142 - 143: 15.212 distance: 143 - 144: 25.414 distance: 143 - 146: 6.948 distance: 144 - 145: 16.792 distance: 144 - 150: 27.871 distance: 146 - 147: 7.515 distance: 147 - 148: 14.781 distance: 147 - 149: 24.262 distance: 150 - 151: 9.590 distance: 150 - 187: 14.185 distance: 151 - 152: 12.136 distance: 151 - 154: 10.473 distance: 152 - 153: 7.077 distance: 152 - 162: 6.930 distance: 153 - 184: 11.763 distance: 154 - 155: 5.706 distance: 155 - 156: 7.055 distance: 155 - 157: 7.000 distance: 156 - 158: 12.383 distance: 157 - 159: 6.204 distance: 158 - 160: 6.695 distance: 159 - 160: 6.677 distance: 160 - 161: 6.976