Starting phenix.real_space_refine on Fri Dec 27 08:53:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y3n_38892/12_2024/8y3n_38892.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y3n_38892/12_2024/8y3n_38892.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y3n_38892/12_2024/8y3n_38892.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y3n_38892/12_2024/8y3n_38892.map" model { file = "/net/cci-nas-00/data/ceres_data/8y3n_38892/12_2024/8y3n_38892.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y3n_38892/12_2024/8y3n_38892.cif" } resolution = 3.8 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= 0.003 sd= 0.026 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 16 5.16 5 C 2321 2.51 5 N 633 2.21 5 O 724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3694 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 917 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 6, 'TRANS': 116} Chain breaks: 1 Chain: "B" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 939 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain breaks: 1 Chain: "C" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 925 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 116} Chain breaks: 1 Chain: "D" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 913 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 116} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 3.11, per 1000 atoms: 0.84 Number of scatterers: 3694 At special positions: 0 Unit cell: (70.3, 94.05, 86.45, 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 16 16.00 O 724 8.00 N 633 7.00 C 2321 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 444.8 milliseconds 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 932 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 5 sheets defined 20.9% alpha, 42.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 97 through 113 removed outlier: 3.566A pdb=" N CYS A 101 " --> pdb=" O THR A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 124 removed outlier: 3.620A pdb=" N SER A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 112 removed outlier: 3.500A pdb=" N LEU B 112 " --> pdb=" O MET B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 124 Processing helix chain 'C' and resid 97 through 112 removed outlier: 3.771A pdb=" N CYS C 101 " --> pdb=" O THR C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 125 Processing helix chain 'D' and resid 97 through 112 Processing helix chain 'D' and resid 116 through 125 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 8 removed outlier: 3.547A pdb=" N PHE A 7 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 20 " --> pdb=" O PHE A 7 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ILE A 33 " --> pdb=" O PRO A 22 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA A 26 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 64 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER A 84 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N TRP A 82 " --> pdb=" O LYS A 66 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 8 removed outlier: 3.547A pdb=" N PHE A 7 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 20 " --> pdb=" O PHE A 7 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ILE A 33 " --> pdb=" O PRO A 22 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA A 26 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU A 90 " --> pdb=" O TYR A 58 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 60 " --> pdb=" O MET A 88 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL A 62 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU B 89 " --> pdb=" O ASN A 87 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU A 89 " --> pdb=" O ASN B 87 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN B 87 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N ARG B 83 " --> pdb=" O PRO A 93 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ALA B 80 " --> pdb=" O ALA B 68 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ALA B 68 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TRP B 82 " --> pdb=" O LYS B 66 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS B 66 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL B 64 " --> pdb=" O SER B 84 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL B 62 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA B 46 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL B 29 " --> pdb=" O PHE B 25 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE B 25 " --> pdb=" O VAL B 29 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLU B 31 " --> pdb=" O SER B 23 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL B 18 " --> pdb=" O LEU B 9 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 7 through 10 removed outlier: 6.736A pdb=" N VAL C 18 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N GLU C 31 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE C 25 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL C 29 " --> pdb=" O PHE C 25 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA C 46 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR C 59 " --> pdb=" O SER C 47 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C 64 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER C 84 " --> pdb=" O VAL C 64 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TRP C 82 " --> pdb=" O LYS C 66 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 7 through 10 removed outlier: 6.736A pdb=" N VAL C 18 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N GLU C 31 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE C 25 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL C 29 " --> pdb=" O PHE C 25 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA C 46 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR C 59 " --> pdb=" O SER C 47 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU D 89 " --> pdb=" O ASN C 87 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU C 89 " --> pdb=" O ASN D 87 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 21 through 26 removed outlier: 7.003A pdb=" N GLU D 31 " --> pdb=" O SER D 23 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N PHE D 25 " --> pdb=" O VAL D 29 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL D 29 " --> pdb=" O PHE D 25 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA D 46 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL D 44 " --> pdb=" O TRP D 32 " (cutoff:3.500A) 179 hydrogen bonds defined for protein. 492 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.94 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1203 1.34 - 1.45: 534 1.45 - 1.57: 1995 1.57 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 3756 Sorted by residual: bond pdb=" CG ASN A 12 " pdb=" OD1 ASN A 12 " ideal model delta sigma weight residual 1.231 1.328 -0.097 1.90e-02 2.77e+03 2.63e+01 bond pdb=" CG ASN D 87 " pdb=" OD1 ASN D 87 " ideal model delta sigma weight residual 1.231 1.326 -0.095 1.90e-02 2.77e+03 2.50e+01 bond pdb=" CG ASN C 116 " pdb=" ND2 ASN C 116 " ideal model delta sigma weight residual 1.328 1.227 0.101 2.10e-02 2.27e+03 2.30e+01 bond pdb=" CG ASN D 87 " pdb=" ND2 ASN D 87 " ideal model delta sigma weight residual 1.328 1.230 0.098 2.10e-02 2.27e+03 2.17e+01 bond pdb=" CG ASN A 12 " pdb=" ND2 ASN A 12 " ideal model delta sigma weight residual 1.328 1.230 0.098 2.10e-02 2.27e+03 2.16e+01 ... (remaining 3751 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 4729 1.34 - 2.69: 298 2.69 - 4.03: 59 4.03 - 5.38: 24 5.38 - 6.72: 7 Bond angle restraints: 5117 Sorted by residual: angle pdb=" C MET A 108 " pdb=" N GLN A 109 " pdb=" CA GLN A 109 " ideal model delta sigma weight residual 120.28 115.24 5.04 1.34e+00 5.57e-01 1.41e+01 angle pdb=" N GLU D 31 " pdb=" CA GLU D 31 " pdb=" C GLU D 31 " ideal model delta sigma weight residual 107.49 113.99 -6.50 1.74e+00 3.30e-01 1.40e+01 angle pdb=" N GLU B 102 " pdb=" CA GLU B 102 " pdb=" C GLU B 102 " ideal model delta sigma weight residual 111.28 107.34 3.94 1.09e+00 8.42e-01 1.31e+01 angle pdb=" CB ASN C 116 " pdb=" CG ASN C 116 " pdb=" ND2 ASN C 116 " ideal model delta sigma weight residual 116.40 121.36 -4.96 1.50e+00 4.44e-01 1.09e+01 angle pdb=" CA GLN C 54 " pdb=" CB GLN C 54 " pdb=" CG GLN C 54 " ideal model delta sigma weight residual 114.10 120.38 -6.28 2.00e+00 2.50e-01 9.87e+00 ... (remaining 5112 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.07: 2001 14.07 - 28.13: 188 28.13 - 42.20: 59 42.20 - 56.27: 14 56.27 - 70.33: 3 Dihedral angle restraints: 2265 sinusoidal: 833 harmonic: 1432 Sorted by residual: dihedral pdb=" CA SER D 52 " pdb=" C SER D 52 " pdb=" N ALA D 53 " pdb=" CA ALA D 53 " ideal model delta harmonic sigma weight residual 180.00 -160.74 -19.26 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA GLN C 50 " pdb=" C GLN C 50 " pdb=" N SER C 51 " pdb=" CA SER C 51 " ideal model delta harmonic sigma weight residual -180.00 -161.06 -18.94 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA SER A 126 " pdb=" C SER A 126 " pdb=" N GLY A 127 " pdb=" CA GLY A 127 " ideal model delta harmonic sigma weight residual -180.00 -162.00 -18.00 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 2262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 328 0.032 - 0.063: 173 0.063 - 0.094: 63 0.094 - 0.126: 39 0.126 - 0.157: 7 Chirality restraints: 610 Sorted by residual: chirality pdb=" CA PRO C 117 " pdb=" N PRO C 117 " pdb=" C PRO C 117 " pdb=" CB PRO C 117 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.17e-01 chirality pdb=" CA PRO B 117 " pdb=" N PRO B 117 " pdb=" C PRO B 117 " pdb=" CB PRO B 117 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA ILE C 60 " pdb=" N ILE C 60 " pdb=" C ILE C 60 " pdb=" CB ILE C 60 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.51e-01 ... (remaining 607 not shown) Planarity restraints: 659 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 116 " 0.039 5.00e-02 4.00e+02 5.83e-02 5.44e+00 pdb=" N PRO B 117 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 117 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 117 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 107 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.54e+00 pdb=" C ALA D 107 " -0.033 2.00e-02 2.50e+03 pdb=" O ALA D 107 " 0.012 2.00e-02 2.50e+03 pdb=" N MET D 108 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN D 116 " 0.028 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO D 117 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 117 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 117 " 0.025 5.00e-02 4.00e+02 ... (remaining 656 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 1463 2.89 - 3.39: 3453 3.39 - 3.89: 5627 3.89 - 4.40: 5947 4.40 - 4.90: 10962 Nonbonded interactions: 27452 Sorted by model distance: nonbonded pdb=" OD1 ASN C 24 " pdb=" N PHE C 25 " model vdw 2.382 3.120 nonbonded pdb=" O TYR D 58 " pdb=" OG1 THR D 59 " model vdw 2.387 3.040 nonbonded pdb=" NH1 ARG A 56 " pdb=" O ASN B 125 " model vdw 2.398 3.120 nonbonded pdb=" ND2 ASN C 12 " pdb=" O GLY C 16 " model vdw 2.399 3.120 nonbonded pdb=" NE2 GLN A 109 " pdb=" O LEU B 112 " model vdw 2.404 3.120 ... (remaining 27447 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 112 or (resid 113 and (name N or name CA or name \ C or name O or name CB )) or resid 114 through 128)) selection = (chain 'B' and (resid 2 through 71 or resid 77 through 112 or (resid 113 and (na \ me N or name CA or name C or name O or name CB )) or resid 114 through 128)) selection = (chain 'C' and (resid 2 through 112 or (resid 113 and (name N or name CA or name \ C or name O or name CB )) or resid 114 through 128)) selection = (chain 'D' and resid 2 through 128) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.340 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 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 : 0.007 0.101 3756 Z= 0.461 Angle : 0.820 6.721 5117 Z= 0.469 Chirality : 0.048 0.157 610 Planarity : 0.006 0.058 659 Dihedral : 13.357 70.333 1333 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.92 % Favored : 88.08 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.37), residues: 478 helix: 0.28 (0.52), residues: 101 sheet: -2.52 (0.38), residues: 159 loop : -2.64 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 32 PHE 0.028 0.003 PHE D 4 TYR 0.012 0.002 TYR B 42 ARG 0.009 0.001 ARG B 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.415 Fit side-chains REVERT: C 27 ASN cc_start: 0.7206 (t0) cc_final: 0.6970 (t0) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1323 time to fit residues: 13.1594 Evaluate side-chains 60 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 4.9990 chunk 36 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN D 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3756 Z= 0.237 Angle : 0.648 9.273 5117 Z= 0.334 Chirality : 0.046 0.133 610 Planarity : 0.005 0.042 659 Dihedral : 5.728 52.499 518 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 0.99 % Allowed : 9.36 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.38), residues: 478 helix: 0.70 (0.51), residues: 102 sheet: -2.01 (0.41), residues: 161 loop : -2.30 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 32 PHE 0.019 0.002 PHE D 4 TYR 0.008 0.001 TYR B 42 ARG 0.003 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.417 Fit side-chains REVERT: A 40 GLN cc_start: 0.8649 (tp40) cc_final: 0.8321 (tp-100) outliers start: 4 outliers final: 3 residues processed: 67 average time/residue: 0.1171 time to fit residues: 10.4632 Evaluate side-chains 56 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 48 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3756 Z= 0.259 Angle : 0.624 6.642 5117 Z= 0.323 Chirality : 0.046 0.137 610 Planarity : 0.005 0.074 659 Dihedral : 5.678 56.835 518 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 0.99 % Allowed : 12.56 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.38), residues: 478 helix: 0.91 (0.50), residues: 101 sheet: -1.71 (0.42), residues: 161 loop : -2.24 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 32 PHE 0.015 0.002 PHE D 4 TYR 0.015 0.001 TYR D 85 ARG 0.002 0.000 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.457 Fit side-chains REVERT: A 6 GLN cc_start: 0.8700 (pp30) cc_final: 0.8368 (pp30) REVERT: A 40 GLN cc_start: 0.8660 (tp40) cc_final: 0.8434 (tp-100) outliers start: 4 outliers final: 3 residues processed: 59 average time/residue: 0.1276 time to fit residues: 10.0383 Evaluate side-chains 55 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain D residue 48 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN B 27 ASN B 40 GLN C 87 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3756 Z= 0.301 Angle : 0.634 8.013 5117 Z= 0.330 Chirality : 0.046 0.143 610 Planarity : 0.005 0.075 659 Dihedral : 5.881 67.659 518 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 2.22 % Allowed : 17.24 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.39), residues: 478 helix: 1.16 (0.51), residues: 101 sheet: -1.68 (0.42), residues: 166 loop : -2.18 (0.41), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 32 PHE 0.016 0.002 PHE D 4 TYR 0.012 0.002 TYR D 85 ARG 0.003 0.000 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.389 Fit side-chains REVERT: A 6 GLN cc_start: 0.8771 (pp30) cc_final: 0.8516 (pp30) REVERT: A 108 MET cc_start: 0.8494 (mmm) cc_final: 0.7198 (mmm) REVERT: A 109 GLN cc_start: 0.7990 (mt0) cc_final: 0.7753 (mp10) REVERT: D 125 ASN cc_start: 0.8042 (OUTLIER) cc_final: 0.7651 (m110) outliers start: 9 outliers final: 6 residues processed: 64 average time/residue: 0.1243 time to fit residues: 10.4664 Evaluate side-chains 60 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 125 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3756 Z= 0.321 Angle : 0.651 7.761 5117 Z= 0.337 Chirality : 0.046 0.143 610 Planarity : 0.005 0.077 659 Dihedral : 6.033 73.676 518 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 2.46 % Allowed : 17.98 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.39), residues: 478 helix: 1.21 (0.52), residues: 101 sheet: -1.65 (0.42), residues: 164 loop : -2.19 (0.40), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 32 PHE 0.014 0.002 PHE D 4 TYR 0.012 0.002 TYR D 85 ARG 0.002 0.000 ARG B 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.450 Fit side-chains REVERT: A 6 GLN cc_start: 0.8794 (pp30) cc_final: 0.8523 (pp30) REVERT: A 40 GLN cc_start: 0.8668 (tp40) cc_final: 0.8413 (tp-100) REVERT: A 108 MET cc_start: 0.8424 (mmm) cc_final: 0.7162 (mmm) REVERT: A 109 GLN cc_start: 0.8019 (mt0) cc_final: 0.7669 (mt0) REVERT: D 125 ASN cc_start: 0.8058 (OUTLIER) cc_final: 0.7656 (m110) outliers start: 10 outliers final: 7 residues processed: 59 average time/residue: 0.1055 time to fit residues: 8.6245 Evaluate side-chains 57 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 125 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3756 Z= 0.338 Angle : 0.654 7.783 5117 Z= 0.340 Chirality : 0.046 0.149 610 Planarity : 0.006 0.079 659 Dihedral : 6.384 86.520 518 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 2.71 % Allowed : 18.97 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.39), residues: 478 helix: 1.15 (0.52), residues: 101 sheet: -1.64 (0.42), residues: 164 loop : -2.19 (0.40), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 32 PHE 0.014 0.002 PHE D 4 TYR 0.012 0.002 TYR D 42 ARG 0.002 0.000 ARG B 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.404 Fit side-chains REVERT: A 6 GLN cc_start: 0.8774 (pp30) cc_final: 0.8559 (pp30) REVERT: A 40 GLN cc_start: 0.8691 (tp40) cc_final: 0.8461 (tp-100) REVERT: A 109 GLN cc_start: 0.8051 (mt0) cc_final: 0.7806 (mt0) REVERT: D 125 ASN cc_start: 0.8072 (OUTLIER) cc_final: 0.7698 (m110) outliers start: 11 outliers final: 7 residues processed: 60 average time/residue: 0.1202 time to fit residues: 9.5862 Evaluate side-chains 59 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 125 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 3756 Z= 0.481 Angle : 0.753 9.183 5117 Z= 0.391 Chirality : 0.048 0.171 610 Planarity : 0.006 0.085 659 Dihedral : 6.742 87.586 518 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.76 % Favored : 87.24 % Rotamer: Outliers : 3.69 % Allowed : 19.46 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.38), residues: 478 helix: 0.91 (0.52), residues: 101 sheet: -1.79 (0.41), residues: 169 loop : -2.43 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP A 32 PHE 0.016 0.003 PHE D 4 TYR 0.013 0.002 TYR B 129 ARG 0.002 0.000 ARG B 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.427 Fit side-chains REVERT: A 40 GLN cc_start: 0.8709 (tp40) cc_final: 0.8476 (tp-100) REVERT: A 109 GLN cc_start: 0.8024 (mt0) cc_final: 0.7693 (mt0) REVERT: D 125 ASN cc_start: 0.8159 (OUTLIER) cc_final: 0.7794 (m110) outliers start: 15 outliers final: 10 residues processed: 69 average time/residue: 0.1187 time to fit residues: 10.9371 Evaluate side-chains 65 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 125 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 42 optimal weight: 0.0270 chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 overall best weight: 1.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3756 Z= 0.239 Angle : 0.653 7.649 5117 Z= 0.338 Chirality : 0.045 0.134 610 Planarity : 0.006 0.085 659 Dihedral : 6.364 87.302 518 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.22 % Allowed : 22.41 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.39), residues: 478 helix: 1.19 (0.51), residues: 101 sheet: -1.58 (0.42), residues: 162 loop : -2.22 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 32 PHE 0.015 0.002 PHE D 4 TYR 0.013 0.002 TYR C 85 ARG 0.002 0.000 ARG B 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.386 Fit side-chains REVERT: D 125 ASN cc_start: 0.7974 (OUTLIER) cc_final: 0.7551 (m110) outliers start: 9 outliers final: 7 residues processed: 59 average time/residue: 0.1243 time to fit residues: 9.7274 Evaluate side-chains 58 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 125 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 0.3980 chunk 38 optimal weight: 0.6980 chunk 40 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3756 Z= 0.165 Angle : 0.613 7.888 5117 Z= 0.318 Chirality : 0.044 0.132 610 Planarity : 0.006 0.081 659 Dihedral : 5.896 84.265 518 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.48 % Allowed : 23.89 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.39), residues: 478 helix: 1.45 (0.51), residues: 101 sheet: -1.28 (0.42), residues: 164 loop : -1.93 (0.42), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 32 PHE 0.012 0.002 PHE C 4 TYR 0.010 0.001 TYR C 85 ARG 0.002 0.000 ARG B 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.409 Fit side-chains REVERT: D 125 ASN cc_start: 0.7920 (OUTLIER) cc_final: 0.7530 (m110) outliers start: 6 outliers final: 5 residues processed: 69 average time/residue: 0.1129 time to fit residues: 10.3452 Evaluate side-chains 66 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 125 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 5.9990 chunk 38 optimal weight: 0.0570 chunk 3 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 23 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 35 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3756 Z= 0.162 Angle : 0.598 8.182 5117 Z= 0.310 Chirality : 0.044 0.129 610 Planarity : 0.006 0.080 659 Dihedral : 5.693 81.150 518 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.48 % Allowed : 25.12 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.39), residues: 478 helix: 1.35 (0.50), residues: 101 sheet: -1.16 (0.41), residues: 176 loop : -1.89 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 32 PHE 0.014 0.002 PHE D 95 TYR 0.009 0.001 TYR C 85 ARG 0.002 0.000 ARG B 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.309 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 65 average time/residue: 0.1195 time to fit residues: 10.2911 Evaluate side-chains 61 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain D residue 48 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 39 optimal weight: 0.2980 chunk 4 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 0.0470 overall best weight: 0.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN D 125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.154556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.125951 restraints weight = 4370.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.127562 restraints weight = 3616.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.128660 restraints weight = 3189.126| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3756 Z= 0.160 Angle : 0.618 10.393 5117 Z= 0.317 Chirality : 0.044 0.129 610 Planarity : 0.006 0.077 659 Dihedral : 5.579 79.382 518 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.23 % Allowed : 25.62 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.39), residues: 478 helix: 1.48 (0.49), residues: 99 sheet: -1.03 (0.41), residues: 176 loop : -1.88 (0.42), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 32 PHE 0.012 0.002 PHE C 4 TYR 0.010 0.001 TYR C 85 ARG 0.002 0.000 ARG B 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1026.89 seconds wall clock time: 19 minutes 52.00 seconds (1192.00 seconds total)