Starting phenix.real_space_refine on Thu Nov 14 10:08:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cio_16683/11_2024/8cio_16683.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cio_16683/11_2024/8cio_16683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cio_16683/11_2024/8cio_16683.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cio_16683/11_2024/8cio_16683.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cio_16683/11_2024/8cio_16683.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cio_16683/11_2024/8cio_16683.cif" } resolution = 3.5 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= 0.002 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 20 5.16 5 C 3485 2.51 5 N 965 2.21 5 O 1185 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 5655 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1131 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 152} Restraints were copied for chains: C, B, E, D Time building chain proxies: 2.70, per 1000 atoms: 0.48 Number of scatterers: 5655 At special positions: 0 Unit cell: (64.428, 64.428, 219.492, 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 20 16.00 O 1185 8.00 N 965 7.00 C 3485 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 85 " distance=2.03 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: 1.40 Conformation dependent library (CDL) restraints added in 824.2 milliseconds 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1390 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 20 sheets defined 0.0% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 29 Processing sheet with id=AA2, first strand: chain 'B' and resid 79 through 80 removed outlier: 3.683A pdb=" N GLY B 76 " --> pdb=" O GLY B 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 79 through 80 removed outlier: 3.683A pdb=" N GLY B 76 " --> pdb=" O GLY B 79 " (cutoff:3.500A) removed outlier: 9.767A pdb=" N ASP B 71 " --> pdb=" O GLY B 61 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLY B 61 " --> pdb=" O ASP B 71 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N GLN B 73 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ASP B 59 " --> pdb=" O GLN B 73 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLN A 34 " --> pdb=" O PHE B 60 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N SER B 62 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL A 36 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY B 170 " --> pdb=" O ILE A 37 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 79 through 80 removed outlier: 3.683A pdb=" N GLY A 76 " --> pdb=" O GLY A 79 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 79 through 80 removed outlier: 3.683A pdb=" N GLY A 76 " --> pdb=" O GLY A 79 " (cutoff:3.500A) removed outlier: 9.766A pdb=" N ASP A 71 " --> pdb=" O GLY A 61 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLY A 61 " --> pdb=" O ASP A 71 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N GLN A 73 " --> pdb=" O ASP A 59 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ASP A 59 " --> pdb=" O GLN A 73 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL D 36 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER A 62 " --> pdb=" O VAL D 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 92 through 95 Processing sheet with id=AA7, first strand: chain 'A' and resid 101 through 102 removed outlier: 3.616A pdb=" N SER A 102 " --> pdb=" O GLN A 105 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN A 105 " --> pdb=" O SER A 102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 26 through 29 Processing sheet with id=AA9, first strand: chain 'C' and resid 79 through 80 removed outlier: 3.684A pdb=" N GLY C 76 " --> pdb=" O GLY C 79 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 79 through 80 removed outlier: 3.684A pdb=" N GLY C 76 " --> pdb=" O GLY C 79 " (cutoff:3.500A) removed outlier: 9.766A pdb=" N ASP C 71 " --> pdb=" O GLY C 61 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLY C 61 " --> pdb=" O ASP C 71 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N GLN C 73 " --> pdb=" O ASP C 59 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ASP C 59 " --> pdb=" O GLN C 73 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N GLN B 34 " --> pdb=" O PHE C 60 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N SER C 62 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL B 36 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY C 170 " --> pdb=" O ILE B 37 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 101 through 102 removed outlier: 3.616A pdb=" N SER B 102 " --> pdb=" O GLN B 105 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN B 105 " --> pdb=" O SER B 102 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 101 through 102 removed outlier: 3.615A pdb=" N SER C 102 " --> pdb=" O GLN C 105 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN C 105 " --> pdb=" O SER C 102 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 79 through 80 removed outlier: 3.683A pdb=" N GLY D 76 " --> pdb=" O GLY D 79 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 79 through 80 removed outlier: 3.683A pdb=" N GLY D 76 " --> pdb=" O GLY D 79 " (cutoff:3.500A) removed outlier: 9.767A pdb=" N ASP D 71 " --> pdb=" O GLY D 61 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY D 61 " --> pdb=" O ASP D 71 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N GLN D 73 " --> pdb=" O ASP D 59 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ASP D 59 " --> pdb=" O GLN D 73 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL E 36 " --> pdb=" O PHE D 60 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER D 62 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY D 170 " --> pdb=" O ILE E 37 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 92 through 95 Processing sheet with id=AB7, first strand: chain 'D' and resid 101 through 102 removed outlier: 3.615A pdb=" N SER D 102 " --> pdb=" O GLN D 105 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN D 105 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 57 through 58 removed outlier: 3.684A pdb=" N GLY E 76 " --> pdb=" O GLY E 79 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 57 through 58 Processing sheet with id=AC1, first strand: chain 'E' and resid 92 through 95 Processing sheet with id=AC2, first strand: chain 'E' and resid 101 through 102 removed outlier: 3.616A pdb=" N SER E 102 " --> pdb=" O GLN E 105 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN E 105 " --> pdb=" O SER E 102 " (cutoff:3.500A) 132 hydrogen bonds defined for protein. 264 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: 1.50 Time building geometry restraints manager: 1.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1905 1.34 - 1.46: 1123 1.46 - 1.57: 2682 1.57 - 1.69: 0 1.69 - 1.80: 30 Bond restraints: 5740 Sorted by residual: bond pdb=" CA THR E 77 " pdb=" CB THR E 77 " ideal model delta sigma weight residual 1.530 1.546 -0.015 1.69e-02 3.50e+03 8.22e-01 bond pdb=" CA THR C 77 " pdb=" CB THR C 77 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 7.85e-01 bond pdb=" CA THR B 77 " pdb=" CB THR B 77 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 7.56e-01 bond pdb=" CA THR A 77 " pdb=" CB THR A 77 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 7.49e-01 bond pdb=" CB ASP C 125 " pdb=" CG ASP C 125 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.43e-01 ... (remaining 5735 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 7712 1.40 - 2.80: 135 2.80 - 4.20: 33 4.20 - 5.59: 5 5.59 - 6.99: 5 Bond angle restraints: 7890 Sorted by residual: angle pdb=" CA THR D 77 " pdb=" CB THR D 77 " pdb=" CG2 THR D 77 " ideal model delta sigma weight residual 110.50 114.10 -3.60 1.70e+00 3.46e-01 4.48e+00 angle pdb=" CA THR A 77 " pdb=" CB THR A 77 " pdb=" CG2 THR A 77 " ideal model delta sigma weight residual 110.50 114.07 -3.57 1.70e+00 3.46e-01 4.41e+00 angle pdb=" CA THR B 77 " pdb=" CB THR B 77 " pdb=" CG2 THR B 77 " ideal model delta sigma weight residual 110.50 114.06 -3.56 1.70e+00 3.46e-01 4.40e+00 angle pdb=" CA THR C 77 " pdb=" CB THR C 77 " pdb=" CG2 THR C 77 " ideal model delta sigma weight residual 110.50 114.06 -3.56 1.70e+00 3.46e-01 4.39e+00 angle pdb=" CA THR E 77 " pdb=" CB THR E 77 " pdb=" CG2 THR E 77 " ideal model delta sigma weight residual 110.50 114.06 -3.56 1.70e+00 3.46e-01 4.39e+00 ... (remaining 7885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.25: 2841 10.25 - 20.51: 301 20.51 - 30.76: 121 30.76 - 41.02: 45 41.02 - 51.27: 15 Dihedral angle restraints: 3323 sinusoidal: 1118 harmonic: 2205 Sorted by residual: dihedral pdb=" CA GLN B 133 " pdb=" CB GLN B 133 " pdb=" CG GLN B 133 " pdb=" CD GLN B 133 " ideal model delta sinusoidal sigma weight residual 180.00 133.78 46.22 3 1.50e+01 4.44e-03 8.30e+00 dihedral pdb=" CA GLN C 133 " pdb=" CB GLN C 133 " pdb=" CG GLN C 133 " pdb=" CD GLN C 133 " ideal model delta sinusoidal sigma weight residual 180.00 133.79 46.21 3 1.50e+01 4.44e-03 8.30e+00 dihedral pdb=" CA GLN A 133 " pdb=" CB GLN A 133 " pdb=" CG GLN A 133 " pdb=" CD GLN A 133 " ideal model delta sinusoidal sigma weight residual 180.00 133.80 46.20 3 1.50e+01 4.44e-03 8.30e+00 ... (remaining 3320 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 630 0.032 - 0.063: 204 0.063 - 0.095: 72 0.095 - 0.127: 84 0.127 - 0.159: 15 Chirality restraints: 1005 Sorted by residual: chirality pdb=" CB THR D 77 " pdb=" CA THR D 77 " pdb=" OG1 THR D 77 " pdb=" CG2 THR D 77 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.29e-01 chirality pdb=" CB THR A 77 " pdb=" CA THR A 77 " pdb=" OG1 THR A 77 " pdb=" CG2 THR A 77 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.99e-01 chirality pdb=" CB THR B 77 " pdb=" CA THR B 77 " pdb=" OG1 THR B 77 " pdb=" CG2 THR B 77 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.93e-01 ... (remaining 1002 not shown) Planarity restraints: 1015 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 151 " 0.017 5.00e-02 4.00e+02 2.58e-02 1.06e+00 pdb=" N PRO B 152 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO B 152 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 152 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 151 " -0.017 5.00e-02 4.00e+02 2.56e-02 1.05e+00 pdb=" N PRO E 152 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO E 152 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO E 152 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 151 " 0.017 5.00e-02 4.00e+02 2.56e-02 1.05e+00 pdb=" N PRO C 152 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO C 152 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 152 " 0.014 5.00e-02 4.00e+02 ... (remaining 1012 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 35 2.61 - 3.18: 5018 3.18 - 3.75: 7807 3.75 - 4.33: 10807 4.33 - 4.90: 18243 Nonbonded interactions: 41910 Sorted by model distance: nonbonded pdb=" SG CYS B 41 " pdb=" SG CYS B 85 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS D 41 " pdb=" SG CYS D 85 " model vdw 2.033 3.760 nonbonded pdb=" SG CYS E 41 " pdb=" SG CYS E 85 " model vdw 2.033 3.760 nonbonded pdb=" SG CYS C 41 " pdb=" SG CYS C 85 " model vdw 2.033 3.760 nonbonded pdb=" O SER E 144 " pdb=" OG1 THR E 145 " model vdw 2.418 3.040 ... (remaining 41905 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 0.910 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.060 Find NCS groups from input model: 0.200 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 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 : 0.002 0.023 5740 Z= 0.152 Angle : 0.547 6.992 7890 Z= 0.284 Chirality : 0.048 0.159 1005 Planarity : 0.003 0.026 1015 Dihedral : 11.522 51.274 1930 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.30), residues: 785 helix: None (None), residues: 0 sheet: 1.41 (0.47), residues: 135 loop : -1.80 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 55 HIS 0.002 0.001 HIS D 100 PHE 0.004 0.001 PHE C 60 TYR 0.006 0.001 TYR B 120 ARG 0.002 0.000 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.591 Fit side-chains REVERT: A 165 PRO cc_start: 0.7375 (Cg_exo) cc_final: 0.7134 (Cg_endo) REVERT: B 84 GLN cc_start: 0.8782 (tm-30) cc_final: 0.8501 (tm-30) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1118 time to fit residues: 19.1696 Evaluate side-chains 78 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 0.0670 chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.7722 ------------------------------------------------------------------------------- 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: 0.8202 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5740 Z= 0.237 Angle : 0.587 8.903 7890 Z= 0.304 Chirality : 0.049 0.143 1005 Planarity : 0.003 0.028 1015 Dihedral : 4.205 17.186 835 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % Rotamer: Outliers : 2.06 % Allowed : 10.79 % Favored : 87.14 % 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: -1.64 (0.30), residues: 785 helix: None (None), residues: 0 sheet: 1.30 (0.46), residues: 135 loop : -1.81 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 182 HIS 0.002 0.001 HIS D 63 PHE 0.009 0.002 PHE C 60 TYR 0.017 0.001 TYR D 107 ARG 0.002 0.001 ARG B 156 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.623 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 94 average time/residue: 0.1094 time to fit residues: 15.6443 Evaluate side-chains 83 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain E residue 100 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 18 optimal weight: 0.0870 chunk 68 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 overall best weight: 1.1560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5740 Z= 0.312 Angle : 0.638 13.432 7890 Z= 0.319 Chirality : 0.050 0.141 1005 Planarity : 0.004 0.028 1015 Dihedral : 4.665 25.716 835 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.57 % Favored : 89.43 % Rotamer: Outliers : 3.65 % Allowed : 13.65 % Favored : 82.70 % 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: -1.76 (0.29), residues: 785 helix: None (None), residues: 0 sheet: 1.07 (0.45), residues: 135 loop : -1.86 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 55 HIS 0.003 0.001 HIS C 63 PHE 0.009 0.002 PHE C 60 TYR 0.010 0.001 TYR D 123 ARG 0.002 0.000 ARG E 128 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.598 Fit side-chains outliers start: 23 outliers final: 13 residues processed: 98 average time/residue: 0.1070 time to fit residues: 15.7876 Evaluate side-chains 81 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain E residue 30 GLN Chi-restraints excluded: chain E residue 100 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 3.9990 chunk 51 optimal weight: 0.0030 chunk 35 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 ASN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5740 Z= 0.262 Angle : 0.623 12.855 7890 Z= 0.310 Chirality : 0.049 0.140 1005 Planarity : 0.004 0.027 1015 Dihedral : 4.611 24.578 835 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.64 % Allowed : 10.45 % Favored : 88.92 % Rotamer: Outliers : 4.29 % Allowed : 16.03 % Favored : 79.68 % 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: -1.77 (0.29), residues: 785 helix: None (None), residues: 0 sheet: 1.04 (0.44), residues: 135 loop : -1.86 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 55 HIS 0.002 0.001 HIS D 63 PHE 0.008 0.001 PHE C 60 TYR 0.010 0.001 TYR D 107 ARG 0.001 0.000 ARG E 106 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 73 time to evaluate : 0.650 Fit side-chains REVERT: A 166 THR cc_start: 0.8619 (OUTLIER) cc_final: 0.8360 (p) outliers start: 27 outliers final: 19 residues processed: 97 average time/residue: 0.1048 time to fit residues: 15.5341 Evaluate side-chains 87 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain E residue 30 GLN Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 100 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 37 optimal weight: 0.0060 chunk 65 optimal weight: 0.4980 chunk 18 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 GLN C 150 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5740 Z= 0.183 Angle : 0.591 12.761 7890 Z= 0.289 Chirality : 0.048 0.139 1005 Planarity : 0.003 0.027 1015 Dihedral : 4.302 23.701 835 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.64 % Allowed : 9.17 % Favored : 90.19 % Rotamer: Outliers : 4.29 % Allowed : 16.67 % Favored : 79.05 % 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: -1.72 (0.29), residues: 785 helix: None (None), residues: 0 sheet: 1.12 (0.45), residues: 135 loop : -1.83 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 182 HIS 0.002 0.001 HIS E 100 PHE 0.006 0.001 PHE C 60 TYR 0.009 0.001 TYR D 107 ARG 0.001 0.000 ARG E 128 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 75 time to evaluate : 0.682 Fit side-chains REVERT: A 166 THR cc_start: 0.8598 (OUTLIER) cc_final: 0.8333 (p) outliers start: 27 outliers final: 17 residues processed: 99 average time/residue: 0.1039 time to fit residues: 15.6989 Evaluate side-chains 87 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 100 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 0.3980 chunk 14 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5740 Z= 0.247 Angle : 0.620 13.877 7890 Z= 0.304 Chirality : 0.049 0.138 1005 Planarity : 0.004 0.027 1015 Dihedral : 4.466 25.591 835 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.64 % Allowed : 11.34 % Favored : 88.03 % Rotamer: Outliers : 3.65 % Allowed : 17.78 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.29), residues: 785 helix: None (None), residues: 0 sheet: 1.04 (0.45), residues: 135 loop : -1.87 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 182 HIS 0.002 0.001 HIS D 63 PHE 0.005 0.001 PHE C 60 TYR 0.008 0.001 TYR D 107 ARG 0.002 0.000 ARG E 128 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.670 Fit side-chains REVERT: A 166 THR cc_start: 0.8642 (OUTLIER) cc_final: 0.8381 (p) outliers start: 23 outliers final: 16 residues processed: 89 average time/residue: 0.1112 time to fit residues: 15.1404 Evaluate side-chains 84 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain E residue 30 GLN Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 100 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 ASN C 73 GLN D 150 ASN E 150 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 5740 Z= 0.307 Angle : 0.648 13.048 7890 Z= 0.323 Chirality : 0.050 0.143 1005 Planarity : 0.004 0.028 1015 Dihedral : 4.810 30.249 835 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.64 % Allowed : 11.21 % Favored : 88.15 % Rotamer: Outliers : 4.44 % Allowed : 17.78 % Favored : 77.78 % 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: -1.90 (0.29), residues: 785 helix: None (None), residues: 0 sheet: 0.92 (0.45), residues: 135 loop : -1.95 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 182 HIS 0.003 0.001 HIS E 63 PHE 0.007 0.002 PHE C 60 TYR 0.010 0.002 TYR B 172 ARG 0.002 0.000 ARG E 106 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 71 time to evaluate : 0.597 Fit side-chains REVERT: A 166 THR cc_start: 0.8598 (OUTLIER) cc_final: 0.8256 (p) REVERT: C 96 ASN cc_start: 0.8375 (OUTLIER) cc_final: 0.8089 (p0) outliers start: 28 outliers final: 20 residues processed: 95 average time/residue: 0.1060 time to fit residues: 15.2707 Evaluate side-chains 90 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 150 ASN Chi-restraints excluded: chain E residue 30 GLN Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 100 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 35 optimal weight: 0.3980 chunk 6 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 65 optimal weight: 0.3980 chunk 69 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 67 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 GLN D 150 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5740 Z= 0.190 Angle : 0.620 13.154 7890 Z= 0.303 Chirality : 0.049 0.139 1005 Planarity : 0.003 0.027 1015 Dihedral : 4.449 27.519 835 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.64 % Allowed : 10.06 % Favored : 89.30 % Rotamer: Outliers : 3.97 % Allowed : 18.89 % Favored : 77.14 % 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: -1.83 (0.29), residues: 785 helix: None (None), residues: 0 sheet: 0.98 (0.45), residues: 135 loop : -1.90 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 182 HIS 0.002 0.001 HIS E 100 PHE 0.004 0.001 PHE C 60 TYR 0.009 0.001 TYR D 107 ARG 0.001 0.000 ARG E 106 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 0.672 Fit side-chains REVERT: A 166 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8335 (p) REVERT: C 41 CYS cc_start: 0.8326 (t) cc_final: 0.8105 (m) REVERT: C 96 ASN cc_start: 0.8324 (OUTLIER) cc_final: 0.8018 (p0) outliers start: 25 outliers final: 16 residues processed: 96 average time/residue: 0.1121 time to fit residues: 16.4388 Evaluate side-chains 89 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 100 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 0.1980 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 67 optimal weight: 0.3980 chunk 44 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 43 optimal weight: 0.1980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5740 Z= 0.181 Angle : 0.620 13.343 7890 Z= 0.301 Chirality : 0.049 0.138 1005 Planarity : 0.003 0.027 1015 Dihedral : 4.242 24.897 835 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.64 % Allowed : 9.94 % Favored : 89.43 % Rotamer: Outliers : 2.86 % Allowed : 19.68 % Favored : 77.46 % 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: -1.81 (0.29), residues: 785 helix: None (None), residues: 0 sheet: 1.03 (0.45), residues: 135 loop : -1.90 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 182 HIS 0.002 0.001 HIS E 100 PHE 0.004 0.001 PHE C 60 TYR 0.009 0.001 TYR E 172 ARG 0.002 0.000 ARG D 128 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.607 Fit side-chains REVERT: A 166 THR cc_start: 0.8671 (OUTLIER) cc_final: 0.8354 (p) REVERT: C 96 ASN cc_start: 0.8276 (OUTLIER) cc_final: 0.7969 (p0) outliers start: 18 outliers final: 15 residues processed: 93 average time/residue: 0.1119 time to fit residues: 15.8059 Evaluate side-chains 91 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 100 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 GLN E 150 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5740 Z= 0.299 Angle : 0.669 13.517 7890 Z= 0.331 Chirality : 0.050 0.142 1005 Planarity : 0.004 0.029 1015 Dihedral : 4.714 29.102 835 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.64 % Allowed : 11.85 % Favored : 87.52 % Rotamer: Outliers : 3.33 % Allowed : 19.84 % Favored : 76.83 % 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 (0.29), residues: 785 helix: None (None), residues: 0 sheet: 0.85 (0.45), residues: 135 loop : -1.97 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 182 HIS 0.003 0.001 HIS D 63 PHE 0.006 0.002 PHE C 60 TYR 0.010 0.002 TYR D 107 ARG 0.002 0.000 ARG E 106 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.645 Fit side-chains REVERT: A 166 THR cc_start: 0.8631 (OUTLIER) cc_final: 0.8317 (p) REVERT: C 41 CYS cc_start: 0.8378 (t) cc_final: 0.8158 (m) REVERT: C 96 ASN cc_start: 0.8350 (OUTLIER) cc_final: 0.8077 (p0) outliers start: 21 outliers final: 16 residues processed: 88 average time/residue: 0.1107 time to fit residues: 14.7719 Evaluate side-chains 85 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 100 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 0.0770 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 0.0170 chunk 61 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.085459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.072808 restraints weight = 12000.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.075491 restraints weight = 6435.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.077335 restraints weight = 4183.878| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5740 Z= 0.169 Angle : 0.634 13.786 7890 Z= 0.305 Chirality : 0.049 0.141 1005 Planarity : 0.003 0.028 1015 Dihedral : 4.249 25.268 835 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.64 % Allowed : 9.04 % Favored : 90.32 % Rotamer: Outliers : 2.86 % Allowed : 20.32 % Favored : 76.83 % 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: -1.84 (0.29), residues: 785 helix: None (None), residues: 0 sheet: 1.03 (0.45), residues: 135 loop : -1.92 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 182 HIS 0.002 0.001 HIS E 100 PHE 0.003 0.001 PHE C 60 TYR 0.009 0.001 TYR D 107 ARG 0.001 0.000 ARG C 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1428.30 seconds wall clock time: 26 minutes 45.80 seconds (1605.80 seconds total)