Starting phenix.real_space_refine on Thu Dec 7 22:00:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr7_34048/12_2023/7yr7_34048.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr7_34048/12_2023/7yr7_34048.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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr7_34048/12_2023/7yr7_34048.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr7_34048/12_2023/7yr7_34048.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr7_34048/12_2023/7yr7_34048.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr7_34048/12_2023/7yr7_34048.pdb" } 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= 0.004 sd= 0.054 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: 5 Type Number sf(0) Gaussians P 118 5.49 5 S 12 5.16 5 C 2731 2.51 5 N 955 2.21 5 O 1286 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F GLU 10": "OE1" <-> "OE2" Residue "F GLU 46": "OE1" <-> "OE2" Residue "E GLU 45": "OE1" <-> "OE2" Residue "G GLU 10": "OE1" <-> "OE2" Residue "D GLU 39": "OE1" <-> "OE2" Residue "D ARG 44": "NH1" <-> "NH2" Residue "D GLU 54": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 5102 Number of models: 1 Model: "" Number of chains: 7 Chain: "F" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 426 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "E" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 426 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "B" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 428 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2547 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 10, 'rna3p_pur': 58, 'rna3p_pyr': 36} Link IDs: {'rna2p': 23, 'rna3p': 94} Chain: "C" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 425 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 52} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 426 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Time building chain proxies: 3.50, per 1000 atoms: 0.69 Number of scatterers: 5102 At special positions: 0 Unit cell: (95.2, 84.15, 112.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 118 15.00 O 1286 8.00 N 955 7.00 C 2731 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 - 3.50 Amino acid : False - 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: 2.41 Conformation dependent library (CDL) restraints added in 488.7 milliseconds 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 598 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 6 sheets defined 17.9% alpha, 16.1% beta 26 base pairs and 49 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'F' and resid 46 through 55 Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'G' and resid 46 through 55 Processing helix chain 'B' and resid 46 through 53 Processing helix chain 'C' and resid 46 through 55 Processing helix chain 'D' and resid 45 through 55 Processing sheet with id=AA1, first strand: chain 'F' and resid 20 through 26 removed outlier: 5.091A pdb=" N ARG F 31 " --> pdb=" O LEU F 23 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N VAL F 25 " --> pdb=" O GLN F 29 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N GLN F 29 " --> pdb=" O VAL F 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 4 through 6 removed outlier: 4.336A pdb=" N LEU E 4 " --> pdb=" O ILE G 32 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE G 32 " --> pdb=" O LEU E 4 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 20 through 26 removed outlier: 4.545A pdb=" N ARG E 31 " --> pdb=" O LEU E 23 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL E 25 " --> pdb=" O GLN E 29 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLN E 29 " --> pdb=" O VAL E 25 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG G 6 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU G 4 " --> pdb=" O ILE E 32 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 20 through 26 removed outlier: 5.224A pdb=" N ARG B 31 " --> pdb=" O LEU B 23 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N VAL B 25 " --> pdb=" O GLN B 29 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLN B 29 " --> pdb=" O VAL B 25 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE B 32 " --> pdb=" O ILE D 3 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 25 through 26 removed outlier: 3.602A pdb=" N LYS C 26 " --> pdb=" O GLN C 29 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 21 through 26 removed outlier: 5.564A pdb=" N VAL D 22 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLY D 33 " --> pdb=" O VAL D 22 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLY D 24 " --> pdb=" O ARG D 31 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN D 29 " --> pdb=" O LYS D 26 " (cutoff:3.500A) 54 hydrogen bonds defined for protein. 153 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 68 hydrogen bonds 124 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 49 stacking parallelities Total time for adding SS restraints: 1.38 Time building geometry restraints manager: 2.58 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: 1154 1.34 - 1.45: 1659 1.45 - 1.57: 2349 1.57 - 1.69: 235 1.69 - 1.81: 24 Bond restraints: 5421 Sorted by residual: bond pdb=" O3' A A 89 " pdb=" P G A 90 " ideal model delta sigma weight residual 1.607 1.662 -0.055 1.50e-02 4.44e+03 1.34e+01 bond pdb=" O3' G A 50 " pdb=" P G A 51 " ideal model delta sigma weight residual 1.607 1.658 -0.051 1.50e-02 4.44e+03 1.17e+01 bond pdb=" O3' C A 62 " pdb=" P A A 63 " ideal model delta sigma weight residual 1.607 1.657 -0.050 1.50e-02 4.44e+03 1.13e+01 bond pdb=" O3' C A 6 " pdb=" P A A 7 " ideal model delta sigma weight residual 1.607 1.654 -0.047 1.50e-02 4.44e+03 9.87e+00 bond pdb=" O3' A A 36 " pdb=" P A A 37 " ideal model delta sigma weight residual 1.607 1.654 -0.047 1.50e-02 4.44e+03 9.72e+00 ... (remaining 5416 not shown) Histogram of bond angle deviations from ideal: 99.30 - 105.91: 715 105.91 - 112.53: 2809 112.53 - 119.15: 1787 119.15 - 125.77: 2147 125.77 - 132.38: 454 Bond angle restraints: 7912 Sorted by residual: angle pdb=" N VAL G 18 " pdb=" CA VAL G 18 " pdb=" C VAL G 18 " ideal model delta sigma weight residual 113.71 107.11 6.60 9.50e-01 1.11e+00 4.83e+01 angle pdb=" O3' C A 76 " pdb=" C3' C A 76 " pdb=" C2' C A 76 " ideal model delta sigma weight residual 109.50 99.30 10.20 1.50e+00 4.44e-01 4.63e+01 angle pdb=" C4' A A 78 " pdb=" C3' A A 78 " pdb=" O3' A A 78 " ideal model delta sigma weight residual 113.00 122.87 -9.87 1.50e+00 4.44e-01 4.33e+01 angle pdb=" C4' A A 75 " pdb=" C3' A A 75 " pdb=" O3' A A 75 " ideal model delta sigma weight residual 113.00 104.18 8.82 1.50e+00 4.44e-01 3.46e+01 angle pdb=" N THR D 19 " pdb=" CA THR D 19 " pdb=" C THR D 19 " ideal model delta sigma weight residual 111.02 118.12 -7.10 1.25e+00 6.40e-01 3.23e+01 ... (remaining 7907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.32: 2963 34.32 - 68.63: 356 68.63 - 102.95: 55 102.95 - 137.27: 1 137.27 - 171.58: 2 Dihedral angle restraints: 3377 sinusoidal: 2449 harmonic: 928 Sorted by residual: dihedral pdb=" O4' C A 62 " pdb=" C1' C A 62 " pdb=" N1 C A 62 " pdb=" C2 C A 62 " ideal model delta sinusoidal sigma weight residual 232.00 60.42 171.58 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" C THR D 19 " pdb=" N THR D 19 " pdb=" CA THR D 19 " pdb=" CB THR D 19 " ideal model delta harmonic sigma weight residual -122.00 -135.66 13.66 0 2.50e+00 1.60e-01 2.99e+01 dihedral pdb=" CA LEU G 2 " pdb=" C LEU G 2 " pdb=" N ILE G 3 " pdb=" CA ILE G 3 " ideal model delta harmonic sigma weight residual -180.00 -152.76 -27.24 0 5.00e+00 4.00e-02 2.97e+01 ... (remaining 3374 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 791 0.100 - 0.200: 176 0.200 - 0.300: 42 0.300 - 0.400: 10 0.400 - 0.500: 1 Chirality restraints: 1020 Sorted by residual: chirality pdb=" CA THR D 19 " pdb=" N THR D 19 " pdb=" C THR D 19 " pdb=" CB THR D 19 " both_signs ideal model delta sigma weight residual False 2.53 2.03 0.50 2.00e-01 2.50e+01 6.24e+00 chirality pdb=" P G A 79 " pdb=" OP1 G A 79 " pdb=" OP2 G A 79 " pdb=" O5' G A 79 " both_signs ideal model delta sigma weight residual True 2.41 -2.76 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CB ILE E 3 " pdb=" CA ILE E 3 " pdb=" CG1 ILE E 3 " pdb=" CG2 ILE E 3 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.86e+00 ... (remaining 1017 not shown) Planarity restraints: 561 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE E 47 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.95e+00 pdb=" C ILE E 47 " 0.046 2.00e-02 2.50e+03 pdb=" O ILE E 47 " -0.017 2.00e-02 2.50e+03 pdb=" N TYR E 48 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 3 " 0.009 2.00e-02 2.50e+03 1.52e-02 6.94e+00 pdb=" N9 G A 3 " -0.013 2.00e-02 2.50e+03 pdb=" C8 G A 3 " -0.011 2.00e-02 2.50e+03 pdb=" N7 G A 3 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G A 3 " 0.009 2.00e-02 2.50e+03 pdb=" C6 G A 3 " 0.024 2.00e-02 2.50e+03 pdb=" O6 G A 3 " 0.003 2.00e-02 2.50e+03 pdb=" N1 G A 3 " -0.039 2.00e-02 2.50e+03 pdb=" C2 G A 3 " 0.013 2.00e-02 2.50e+03 pdb=" N2 G A 3 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G A 3 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G A 3 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA F 36 " 0.043 5.00e-02 4.00e+02 6.48e-02 6.72e+00 pdb=" N PRO F 37 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO F 37 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 37 " 0.036 5.00e-02 4.00e+02 ... (remaining 558 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 1653 2.89 - 3.39: 4213 3.39 - 3.89: 9409 3.89 - 4.40: 9604 4.40 - 4.90: 13814 Nonbonded interactions: 38693 Sorted by model distance: nonbonded pdb=" OG1 THR G 21 " pdb=" O GLY G 33 " model vdw 2.385 2.440 nonbonded pdb=" O5' A A 49 " pdb=" O4' A A 49 " model vdw 2.438 2.432 nonbonded pdb=" O THR E 5 " pdb=" OG1 THR E 5 " model vdw 2.445 2.440 nonbonded pdb=" O5' C A 6 " pdb=" O4' C A 6 " model vdw 2.447 2.432 nonbonded pdb=" N2 G A 40 " pdb=" O ALA D 36 " model vdw 2.448 2.520 ... (remaining 38688 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 1 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 22 or (resid 23 through 24 and (nam \ e N or name CA or name C or name O )) or resid 25 or (resid 26 and (name N or na \ me CA or name C or name O or name CB )) or resid 27 through 55)) selection = (chain 'C' and (resid 1 through 22 or (resid 23 through 24 and (name N or name C \ A or name C or name O )) or resid 25 or (resid 26 and (name N or name CA or name \ C or name O or name CB )) or resid 27 through 55)) selection = (chain 'D' and (resid 1 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 22 or (resid 23 through 24 and (nam \ e N or name CA or name C or name O )) or resid 25 through 55)) selection = (chain 'E' and (resid 1 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 25 or (resid 26 and (name N or name \ CA or name C or name O or name CB )) or resid 27 through 55)) selection = (chain 'F' and (resid 1 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 22 or (resid 23 through 24 and (nam \ e N or name CA or name C or name O )) or resid 25 through 55)) selection = (chain 'G' and (resid 1 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 22 or (resid 23 through 24 and (nam \ e N or name CA or name C or name O )) or resid 25 through 55)) } 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: 0.010 Normalize map: mean=0, sd=1: 0.490 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: 2.560 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.170 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5926 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 : 0.008 0.055 5421 Z= 0.474 Angle : 1.253 10.451 7912 Z= 0.759 Chirality : 0.094 0.500 1020 Planarity : 0.008 0.065 561 Dihedral : 25.243 171.582 2779 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 4.74 % Allowed : 12.77 % Favored : 82.48 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % 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: -5.36 (0.35), residues: 318 helix: -4.63 (0.31), residues: 54 sheet: -4.54 (0.75), residues: 20 loop : -3.53 (0.33), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS E 43 TYR 0.023 0.003 TYR E 48 ARG 0.006 0.001 ARG E 6 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 109 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 114 average time/residue: 0.2378 time to fit residues: 32.1700 Evaluate side-chains 90 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 0.348 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1849 time to fit residues: 1.7513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 chunk 12 optimal weight: 0.0570 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 28 ASN F 29 GLN G 35 ASN B 35 ASN B 43 HIS ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN D 52 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5961 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5421 Z= 0.169 Angle : 0.655 7.614 7912 Z= 0.339 Chirality : 0.041 0.229 1020 Planarity : 0.004 0.042 561 Dihedral : 25.356 172.454 2147 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.04 % Favored : 83.96 % Rotamer: Outliers : 4.38 % Allowed : 25.18 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % 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: -4.45 (0.39), residues: 318 helix: -2.79 (0.53), residues: 55 sheet: -3.83 (0.80), residues: 20 loop : -3.20 (0.35), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS F 43 TYR 0.008 0.001 TYR E 48 ARG 0.005 0.001 ARG E 44 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 102 average time/residue: 0.2219 time to fit residues: 27.1095 Evaluate side-chains 89 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 83 time to evaluate : 0.378 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0518 time to fit residues: 0.9874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 37 optimal weight: 0.2980 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 0.0370 chunk 36 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 overall best weight: 2.8664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 29 GLN G 35 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6152 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5421 Z= 0.274 Angle : 0.764 8.304 7912 Z= 0.392 Chirality : 0.044 0.193 1020 Planarity : 0.005 0.038 561 Dihedral : 25.645 176.976 2147 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 21.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.13 % Favored : 79.87 % Rotamer: Outliers : 5.11 % Allowed : 26.28 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -3.97 (0.44), residues: 318 helix: -2.03 (0.57), residues: 55 sheet: -3.74 (0.76), residues: 30 loop : -2.86 (0.41), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS D 43 TYR 0.019 0.002 TYR E 48 ARG 0.011 0.001 ARG E 6 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 90 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 98 average time/residue: 0.2027 time to fit residues: 24.5715 Evaluate side-chains 91 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 0.397 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0476 time to fit residues: 1.1597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.0670 chunk 28 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6058 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5421 Z= 0.166 Angle : 0.627 8.371 7912 Z= 0.318 Chirality : 0.040 0.185 1020 Planarity : 0.004 0.032 561 Dihedral : 25.345 179.307 2147 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.41 % Favored : 84.59 % Rotamer: Outliers : 4.01 % Allowed : 29.20 % Favored : 66.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -3.33 (0.47), residues: 318 helix: -1.42 (0.63), residues: 55 sheet: -2.65 (1.08), residues: 20 loop : -2.59 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 43 TYR 0.009 0.001 TYR E 48 ARG 0.014 0.001 ARG G 6 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 95 average time/residue: 0.1938 time to fit residues: 22.6601 Evaluate side-chains 86 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 0.383 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0514 time to fit residues: 1.0871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 ASN D 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6272 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 5421 Z= 0.382 Angle : 0.899 11.188 7912 Z= 0.456 Chirality : 0.049 0.209 1020 Planarity : 0.006 0.035 561 Dihedral : 26.025 171.017 2147 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 30.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.90 % Favored : 76.10 % Rotamer: Outliers : 7.30 % Allowed : 27.74 % Favored : 64.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.63 % 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: -3.78 (0.46), residues: 318 helix: -2.06 (0.61), residues: 55 sheet: -3.33 (1.22), residues: 20 loop : -2.79 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS D 43 TYR 0.023 0.002 TYR E 48 ARG 0.010 0.001 ARG G 6 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 85 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 14 residues processed: 98 average time/residue: 0.1677 time to fit residues: 20.8835 Evaluate side-chains 96 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 0.385 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0806 time to fit residues: 2.1307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6221 moved from start: 0.5107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5421 Z= 0.269 Angle : 0.772 11.247 7912 Z= 0.385 Chirality : 0.044 0.173 1020 Planarity : 0.005 0.030 561 Dihedral : 25.790 174.742 2147 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 25.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.07 % Favored : 78.93 % Rotamer: Outliers : 5.11 % Allowed : 28.10 % Favored : 66.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -3.62 (0.46), residues: 318 helix: -1.90 (0.61), residues: 55 sheet: -4.65 (1.30), residues: 10 loop : -2.67 (0.41), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS E 43 TYR 0.018 0.002 TYR E 48 ARG 0.009 0.001 ARG G 6 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 84 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 93 average time/residue: 0.2065 time to fit residues: 23.6096 Evaluate side-chains 90 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 0.400 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1024 time to fit residues: 1.7626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 33 optimal weight: 0.4980 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6215 moved from start: 0.5425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5421 Z= 0.270 Angle : 0.791 11.340 7912 Z= 0.391 Chirality : 0.045 0.197 1020 Planarity : 0.005 0.048 561 Dihedral : 25.795 174.471 2147 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 26.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.01 % Favored : 77.99 % Rotamer: Outliers : 2.92 % Allowed : 28.47 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -3.53 (0.46), residues: 318 helix: -1.76 (0.61), residues: 55 sheet: -4.48 (1.42), residues: 10 loop : -2.63 (0.41), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS D 43 TYR 0.018 0.002 TYR E 48 ARG 0.011 0.001 ARG E 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 86 average time/residue: 0.1862 time to fit residues: 20.1771 Evaluate side-chains 83 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 0.378 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1583 time to fit residues: 1.2383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 0.0980 chunk 31 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 ASN B 28 ASN B 35 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6060 moved from start: 0.5460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 5421 Z= 0.160 Angle : 0.638 9.233 7912 Z= 0.313 Chirality : 0.039 0.176 1020 Planarity : 0.003 0.027 561 Dihedral : 25.287 179.282 2147 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.41 % Favored : 84.59 % Rotamer: Outliers : 2.19 % Allowed : 31.02 % Favored : 66.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % 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: -3.05 (0.47), residues: 318 helix: -1.32 (0.62), residues: 55 sheet: -2.28 (1.65), residues: 10 loop : -2.40 (0.41), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 43 TYR 0.012 0.001 TYR E 48 ARG 0.005 0.000 ARG G 6 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 87 average time/residue: 0.1997 time to fit residues: 21.3564 Evaluate side-chains 77 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 75 time to evaluate : 0.348 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0482 time to fit residues: 0.5903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 37 optimal weight: 0.0980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 ASN B 35 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6134 moved from start: 0.5630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 5421 Z= 0.209 Angle : 0.702 9.959 7912 Z= 0.344 Chirality : 0.041 0.222 1020 Planarity : 0.004 0.030 561 Dihedral : 25.434 177.193 2147 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 20.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.18 % Favored : 80.82 % Rotamer: Outliers : 1.09 % Allowed : 33.58 % Favored : 65.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -3.32 (0.46), residues: 318 helix: -1.51 (0.60), residues: 55 sheet: -3.27 (1.09), residues: 20 loop : -2.48 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 43 TYR 0.015 0.002 TYR E 48 ARG 0.008 0.001 ARG G 6 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 83 average time/residue: 0.2033 time to fit residues: 20.9199 Evaluate side-chains 82 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 80 time to evaluate : 0.449 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0511 time to fit residues: 0.6768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.0170 chunk 3 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 4 optimal weight: 0.4980 chunk 13 optimal weight: 0.0030 chunk 33 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 overall best weight: 0.4230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5963 moved from start: 0.5817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 5421 Z= 0.157 Angle : 0.651 10.414 7912 Z= 0.318 Chirality : 0.039 0.201 1020 Planarity : 0.004 0.041 561 Dihedral : 25.088 179.559 2147 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.78 % Favored : 85.22 % Rotamer: Outliers : 1.09 % Allowed : 33.58 % Favored : 65.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % 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: -3.10 (0.45), residues: 318 helix: -1.58 (0.56), residues: 55 sheet: -2.08 (1.74), residues: 10 loop : -2.39 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 43 TYR 0.010 0.001 TYR E 48 ARG 0.007 0.001 ARG C 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 79 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 80 average time/residue: 0.2085 time to fit residues: 20.5059 Evaluate side-chains 80 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 0.374 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0481 time to fit residues: 0.6255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 10.0000 chunk 1 optimal weight: 0.3980 chunk 23 optimal weight: 8.9990 chunk 37 optimal weight: 0.0000 chunk 21 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.178595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.143121 restraints weight = 13583.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.146758 restraints weight = 8326.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.149264 restraints weight = 5985.414| |-----------------------------------------------------------------------------| r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6487 moved from start: 0.5944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5421 Z= 0.246 Angle : 0.748 10.985 7912 Z= 0.370 Chirality : 0.043 0.230 1020 Planarity : 0.005 0.055 561 Dihedral : 25.479 176.652 2147 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 23.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.07 % Favored : 78.93 % Rotamer: Outliers : 1.09 % Allowed : 34.31 % Favored : 64.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -3.46 (0.44), residues: 318 helix: -1.83 (0.57), residues: 55 sheet: -3.23 (1.11), residues: 20 loop : -2.54 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS E 43 TYR 0.016 0.001 TYR E 48 ARG 0.011 0.001 ARG C 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1259.36 seconds wall clock time: 23 minutes 24.51 seconds (1404.51 seconds total)